Comparative Genomics of 9 Novel Paenibacillus Larvae Bacteriophages

American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 30 overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area

Identification of nitrifying bacteria contained in a commercial inoculant using molecular biology techniques

Nitrifying bacteria play an important role in aquatic and terrestrial environments through the nitrogen cycle. Nitrification, one of the processes of the nitrogen cycle, refers to the oxidation of ammonia to nitrate. This process requires two types of chemoautotrophic bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). These bacteria are essential in maintaining an optimal environment for plants and aquatic organisms, such as fish. Current applications of nitrifiers include: inoculants for aquariums, biofertilizers, and nitrogen removal in wastewater treatment plants. This study wants to identify a consortium of nitrifers that can be used to produce sufficient nitrate for plants in a hydroponic system. Previous studies have shown that Fritz-zyme turbostart 700, a commercial freshwater inoculant has had success in a semi-hydroponic system, zeoponics. Our lab’s preliminary data has shown that Fritz-zyme contains more than the specific nitrifying bacteria. In order to create the optimal consortium, it would be mandatory that we know exactly what bacteria we are working with. Using 16s rDNA universal primers and PGEM-T easy vector cloning kit, this study will amplify the 16s rDNA present in different enrichment samples and clone it into the PGEM-T easy vector E. coli plasmid. The cloned plasmids are transformed into competent E. coli cells and sequenced to identify the bacteria present in each sample. This study will determine whether the current enrichment techniques being used are sufficient to eliminate the heterotrophic and sporeforming bacteria present in the original Fritz-zyme

Humidity and temperature boundaries for biofilm formation in Yucca Mountain

To determine the long-term success of the recommended Yucca Mountain high-level nuclear waste repository, studies of bacterial colonization and biofilm development are needed. Bacteria involved in microbially-influenced corrosion and degradation are known to form biofilms with the potential to impact the integrity of repository packaging and structural materials. Temperature and humidity are environmental factors that can greatly affect biofilm formation. Therefore, it is necessary to determine the temperature and humidity conditions that affect biofilm formation. Microcosms, which simulated the repository environment of Yucca Mountain, were placed at temperatures ranging from 30° C to 70° C and in relative humidities ranging from 100% to 32%. The microcosms contained titanium, C22 nickel alloy, and N316 stainless steel coupons buried in crushed Yucca Mountain muckpile rock. The uniform-sized metal coupons were sacrificed at the following timepoints: day 0, 1 day, 1 month, 5 months,! year, and 18 months. The average number of culturable bacteria harvested from the entire surface of each of the three coupon types, incubated at 100% relative humidity and 30° C, increased from approximately 1x102 CPU at day 0 to a range of 4-7x104 CPU at 5 months, followed by a decrease to 5-8x102 CPU after 18 months of incubation. The average number of culturable bacteria harvested from the surfaces of the three metals, incubated at 84%, 70.5%, and 32% relative humidity and 30° C, were unchanged at 102 CPU from day 0 to 18 months or decreased to numbers below the level of detection. Culturable bacterial counts, from the three candidate metals incubated at 60 and 70° C and 100% relative humidity, showed a decrease from 102 CPU at day 0 to numbers below the level of detection at 18 months. Confocal laser microscopy 6 showed minimal differences in the extent of microbial colonization on the three metal surfaces in all but optimum conditions, 100% RH and 30° C, at each timepoint after day zero. These data indicate that a decrease in relative humidity level or an increase in temperature severely affects biofilm formation on the three candidate metals being considered for repository packaging at the recommended Yucca Mountain nuclear waste repository

Observed deep cyclonic eddies around Southern Greenland

Author Posting. © American Meteorological Society, 2021. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 51(10), (2021): 3235–3252, https://doi.org/10.1175/JPO-D-20-0288.1.Recent mooring measurements from the Overturning in the Subpolar North Atlantic Program have revealed abundant cyclonic eddies at both sides of Cape Farewell, the southern tip of Greenland. In this study, we present further observational evidence, from both Eulerian and Lagrangian perspectives, of deep cyclonic eddies with intense rotation (ζ/f > 1) around southern Greenland and into the Labrador Sea. Most of the observed cyclones exhibit strongest rotation below the surface at 700–1000 dbar, where maximum azimuthal velocities are ~30 cm s−1 at radii of ~10 km, with rotational periods of 2–3 days. The cyclonic rotation can extend to the deep overflow water layer (below 1800 dbar), albeit with weaker azimuthal velocities (~10 cm s−1) and longer rotational periods of about one week. Within the middepth rotation cores, the cyclones are in near solid-body rotation and have the potential to trap and transport water. The first high-resolution hydrographic transect across such a cyclone indicates that it is characterized by a local (both vertically and horizontally) potential vorticity maximum in its middepth core and cold, fresh anomalies in the deep overflow water layer, suggesting its source as the Denmark Strait outflow. Additionally, the propagation and evolution of the cyclonic eddies are illustrated with deep Lagrangian floats, including their detachments from the boundary currents to the basin interior. Taken together, the combined Eulerian and Lagrangian observations have provided new insights on the boundary current variability and boundary–interior exchange over a geographically large scale near southern Greenland, calling for further investigations on the (sub)mesoscale dynamics in the region.OOI mooring data are based upon work supported by the National Science Foundation under Cooperative Agreement 1743430. S. Zou, A. Bower, and H. Furey gratefully acknowledge the support from the Physical Oceanography Program of the U.S. National Science Foundation Grant OCE-1756361. R.S. Pickart acknowledges support from National Science Foundation Grants OCE-1259618 and OCE-1756361. N. P. Holliday and L. Houpert were supported by NERC programs U.K. OSNAP (NE/K010875) and U.K. OSNAP-Decade (NE/T00858X/1)

Isolation and characterization of thermophilic, calcium-precipitating bacteria form calcite deposits at Yucca Mountain

Calcite deposits, composed of a mixture of calcium carbonate and silicon dioxide, were found in fractures and small cavities within the welded tuff of Yucca Mountain. This research investigation involves determining the presence of thermophilic, calciumprecipitating bacteria within these deposits. The possible existence of thermophilic bacteria may help to resolve the issue of whether these calcite deposits formed from precipitation of dissolved calcium carbonate in rain water transported from the overlying soil environment or as a result of upwelling of geothermally-heated waters transported from below the mountain. Evidence for microbially-influenced calcite precipitation in these deposits is indicated by the presence of moderately-thermophilic, calciumprecipitating bacteria. Growth of bacteria enriched from crushed calcite and calcite/tuff mixed samples collected from tunnels within Yucca Mountain indicate a tendency for thermophiles to be found in calcite deposits and mixed rock samples compared to tuff samples (no calcite) which lacked bacterial growth at temperatures of 50° C and higher. Calcite isolates growing at 60 and 70° C were identified as thermophiles, the most common identification being Bacillus stearothermophilus. SEM and electron dispersion spectroscopy (EDS) results showed that bacteria, isolated from Yucca Mountain calcite and calcite/tuff, produced calcite (CaCO3) when grown on calcium-enriched medium. This evidence indicates a possible warm water influence in the history of Yucca Mountain

Discordant Risk: Overweight and cardiometabolic risk in Chinese adults

Recent US work identifies “metabolically healthy overweight” and “metabolically at risk normal weight” individuals. Less is known for modernizing countries with recent increased obesity. Fasting blood samples, anthropometry and blood pressure from 8,233 adults aged 18–98 in the 2009 nationwide China Health and Nutrition Survey, were used to determine prevalence of overweight (Asian cut point, BMI≥23 kg/m2) and five risk factors [pre-diabetes/diabetes (HbA1c≥5.7%) inflammation (hsCRP ≥3 mg/L), pre-hypertension/hypertension (SBP/DBP≥130/85 mmHg), high triglycerides (≥150 mg/dL), low high-density lipoprotein cholesterol (70 years: 73%). Abdominal obesity was highly predictive of metabolic risk, irrespective of overweight (e.g., “metabolically at risk overweight” relative to “metabolically healthy normal weight” [men: Relative Risk Ratio (RRR) =39.06; 95% Confidence Interval (CI): 23.47, 65.00; women: RRR=22.26; 95% CI: 17.49, 28.33]). To conclude, a large proportion of Chinese adults have metabolic abnormalities. High hypertension risk with age, irrespective of obesity underlies the low prevalence of metabolically healthy overweight. Screening for cardiometabolic-related outcomes dependent upon overweight will likely miss a large portion of the Chinese at-risk population

Observed deep cyclonic eddies around Southern Greenland

Recent mooring measurements from the Overturning in the Subpolar North Atlantic Program have revealed abundant cyclonic eddies at both sides of Cape Farewell, the southern tip of Greenland. In this study, we present further observational evidence, from both Eulerian and Lagrangian perspectives, of deep cyclonic eddies with intense rotation (ζ/f > 1) around southern Greenland and into the Labrador Sea. Most of the observed cyclones exhibit strongest rotation below the surface at 700–1000 dbar, where maximum azimuthal velocities are ~30 cm s−1 at radii of ~10 km, with rotational periods of 2–3 days. The cyclonic rotation can extend to the deep overflow water layer (below 1800 dbar), albeit with weaker azimuthal velocities (~10 cm s−1) and longer rotational periods of about one week. Within the middepth rotation cores, the cyclones are in near solid-body rotation and have the potential to trap and transport water. The first high-resolution hydrographic transect across such a cyclone indicates that it is characterized by a local (both vertically and horizontally) potential vorticity maximum in its middepth core and cold, fresh anomalies in the deep overflow water layer, suggesting its source as the Denmark Strait outflow. Additionally, the propagation and evolution of the cyclonic eddies are illustrated with deep Lagrangian floats, including their detachments from the boundary currents to the basin interior. Taken together, the combined Eulerian and Lagrangian observations have provided new insights on the boundary current variability and boundary–interior exchange over a geographically large scale near southern Greenland, calling for further investigations on the (sub)mesoscale dynamics in the region

Longitudinal associations of away-from-home eating, snacking, screen time, and physical activity behaviors with cardiometabolic risk factors among Chinese children and their parents

Background: Little is known about intergenerational differences in associations of urbanization-related lifestyle behaviors with cardiometabolic risk factors in children and their parents in rapidly urbanizing China

Discordant Risk: Overweight and Cardiometabolic Risk in Chinese Adults

Recent US work identifies “metabolically healthy overweight” and “metabolically at risk normal weight” individuals. Less is known for modernizing countries with recent increased obesity. Fasting blood samples, anthropometry and blood pressure from 8,233 adults aged 18–98 in the 2009 nationwide China Health and Nutrition Survey, were used to determine prevalence of overweight (Asian cut point, BMI≥23 kg/m2) and five risk factors [pre-diabetes/diabetes (HbA1c≥5.7%) inflammation (hsCRP ≥3 mg/L), pre-hypertension/hypertension (SBP/DBP≥130/85 mmHg), high triglycerides (≥150 mg/dL), low high-density lipoprotein cholesterol (70 years: 73%). Abdominal obesity was highly predictive of metabolic risk, irrespective of overweight (e.g., “metabolically at risk overweight” relative to “metabolically healthy normal weight” [men: Relative Risk Ratio (RRR) =39.06; 95% Confidence Interval (CI): 23.47, 65.00; women: RRR=22.26; 95% CI: 17.49, 28.33]). To conclude, a large proportion of Chinese adults have metabolic abnormalities. High hypertension risk with age, irrespective of obesity underlies the low prevalence of metabolically healthy overweight. Screening for cardiometabolic-related outcomes dependent upon overweight will likely miss a large portion of the Chinese at-risk population

Bodyweight Perceptions among Texas Women: The Effects of Religion, Race/Ethnicity, and Citizenship Status

Despite previous work exploring linkages between religious participation and health, little research has looked at the role of religion in affecting bodyweight perceptions. Using the theoretical model developed by Levin et al. (Sociol Q 36(1):157–173, 1995) on the multidimensionality of religious participation, we develop several hypotheses and test them by using data from the 2004 Survey of Texas Adults. We estimate multinomial logistic regression models to determine the relative risk of women perceiving themselves as overweight. Results indicate that religious attendance lowers risk of women perceiving themselves as very overweight. Citizenship status was an important factor for Latinas, with noncitizens being less likely to see themselves as overweight. We also test interaction effects between religion and race. Religious attendance and prayer have a moderating effect among Latina non-citizens so that among these women, attendance and prayer intensify perceptions of feeling less overweight when compared to their white counterparts. Among African American women, the effect of increased church attendance leads to perceptions of being overweight. Prayer is also a correlate of overweight perceptions but only among African American women. We close with a discussion that highlights key implications from our findings, note study limitations, and several promising avenues for future research