Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome.

Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.

Hot spots for allosteric regulation on protein surfaces.

Recent work indicates a general architecture for proteins in which sparse networks of physically contiguous and coevolving amino acids underlie basic aspects of structure and function. These networks, termed sectors, are spatially organized such that active sites are linked to many surface sites distributed throughout the structure. Using the metabolic enzyme dihydrofolate reductase as a model system, we show that: (1) the sector is strongly correlated to a network of residues undergoing millisecond conformational fluctuations associated with enzyme catalysis, and (2) sector-connected surface sites are statistically preferred locations for the emergence of allosteric control in vivo. Thus, sectors represent an evolutionarily conserved "wiring" mechanism that can enable perturbations at specific surface positions to rapidly initiate conformational control over protein function. These findings suggest that sectors enable the evolution of intermolecular communication and regulation.

Constructing and interpreting a large-scale variant effect map for an ultrarare disease gene: Comprehensive prediction of the functional impact of PSAT1 genotypes.

Reduced activity of the enzymes encoded by PHGDH, PSAT1, and PSPH causes a set of ultrarare, autosomal recessive diseases known as serine biosynthesis defects. These diseases present in a broad phenotypic spectrum: at the severe end is Neu-Laxova syndrome, in the intermediate range are infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end is childhood disease with intellectual disability. However, L-serine supplementation, especially if started early, can ameliorate and in some cases even prevent symptoms. Therefore, knowledge of pathogenic variants can improve clinical outcomes. Here, we use a yeast-based assay to individually measure the functional impact of 1,914 SNV-accessible amino acid substitutions in PSAT. Results of our assay agree well with clinical interpretations and protein structure-function relationships, supporting the inclusion of our data as functional evidence as part of the ACMG variant interpretation guidelines. We use existing ClinVar variants, disease alleles reported in the literature and variants present as homozygotes in the primAD database to define assay ranges that could aid clinical variant interpretation for up to 98% of the tested variants. In addition to measuring the functional impact of individual variants in yeast haploid cells, we also assay pairwise combinations of PSAT1 alleles that recapitulate human genotypes, including compound heterozygotes, in yeast diploids. Results from our diploid assay successfully distinguish the genotypes of affected individuals from those of healthy carriers and agree well with disease severity. Finally, we present a linear model that uses individual allele measurements to predict the biallelic function of ~1.8 million allele combinations corresponding to potential human genotypes. Taken together, our work provides an example of how large-scale functional assays in model systems can be powerfully applied to the study of ultrarare diseases.

Isolation of a CTX-M-55 (ESBL)-Producing Escherichia coli Strain of the Global ST6448 Clone from a Captive Orangutan in the USA.

The purpose of this study was to determine if orangutans (Pongo spp.) living in captivity at a zoo in Wisconsin were colonized with antimicrobial-resistant bacteria and, if found, to identify underlying genetic mechanisms contributing to their resistant phenotypes. We hypothesize that since antimicrobial-resistant bacteria are so prevalent within humans, the animals could also be carriers of such strains given the daily contact between the animals and the zoo staff that care for them. To test this theory, fecal samples from two orangutans were examined for resistant bacteria by inoculation on HardyCHROM™ ESBL and HardyCHROM™ CRE agars. Isolates were identified using MALDI-TOF mass spectrometry and antimicrobial susceptibility testing was performed using a Microscan autoSCAN-4 System. An isolate was selected for additional characterization, including whole genome sequencing (WGS). Using the Type (Strain) Genome Server (TYGS) the bacterium was identified as Escherichia coli. The sequence type identified was (ST/phylogenetic group/ß-lactamase): ST6448/B1/CTX-M-55.

Pantoea leporis sp. nov., isolated from the faecal material of a rabbit.

A facultative anaerobic, Gram-stain-negative rod-shaped bacterium, designated RT, was isolated from the faecal material of a rabbit (Sylvilagus floridanus). The strain could not be identified using an MALDI Biotyper sirius CA System. The closest matches based on the Bruker library were members of the genera Citrobacter and Pantoea. However, the score value was in the range of no organism identification possible. Based on pairwise of 16S rRNA gene sequence analysis, the isolate was found to be a member of the family Erwiniaceae. The highest sequence similarities were found to the sequences of Pantoea rodasii LMG 26273T (98.7 %), Leclercia adecarboxylata NBRC 102595T (98.5 %) and Enterobacter huaxiensis 090008T (98.4 %). Phylogenetic and whole genome analysis demonstrated that strain RT represents a novel species within the genus Pantoea. The predominant cellular fatty acids of strain RT were C16 : 0 and products present in summed feature 2 (C12 : 0) aldehyde, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). In silico genome analysis showed the presence of enzymes required for production of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The G+C content determined from the genome was 54.94 mol %. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Pantoea for which the name Pantoea leporis sp. nov. is proposed. The type strain is strain RT (=CCUG 76269T=ATCC TSD-291T).

Robinsoniella peoriensis: an emerging pathogen with few virulence factors.

Robinsoniella peoriensis is a Gram-positive bacterium which is anaerobic, spore-forming, and non-motile. It was initially isolated and characterized from feces and swine manure. Strains of this species have since been identified from different mammalian and non-mammalian gastrointestinal tracts. Strains have also been isolated from a variety of human infections, such as bacteremia, bone infections, and skin structures. R. peoriensis has recently been reported as causative for pyometra, which could result in death in the absence of sufficient antimicrobial treatment. However, to the author's knowledge, there has not been a single virulence factor identified. A major challenge of modern medicine is the failure of conventional procedures to characterize the capability of an emerging pathogen to cause disease. The goal of this study is to initially characterize the pathogenicity of this bacterium using a pathogenomics approach.

The intestinal microbiota of a Risso's dolphin (Grampus griseus): possible relationships with starvation raised by macro-plastic ingestion.

Ingesting marine plastics is increasingly common in cetaceans, but little is known about their potential effects. Here, by utilizing 16S rRNA gene sequencing, we profiled the intestinal bacterial communities of a stranded Risso's dolphin (Grampus griseus) which died because of the ingestion of rubber gloves. In this study, we explored the potential relationships between starvation raised by plastic ingestion with the dolphin gut microbiota. Our results showed significant differences in bacterial diversity and composition among the different anatomical areas along the intestinal tract, which may be related to the intestinal emptying process under starvation. In addition, the intestinal bacterial composition of the Risso's dolphin showed both similarity and divergence to that of other toothed whales, suggesting potential roles of both host phylogeny and habitat shaping of the cetacean intestinal microbiome. Perhaps, the microbiota is reflecting a potentially disordered intestinal microbial profile caused by the ingestion of macro-plastics which led to starvation. Moreover, two operational taxonomic units (0.17% of the total reads) affiliated with Actinobacillus and Acinetobacter lwoffii were detected along the intestinal tract. These bacterial species may cause infections in immunocompromised dolphins which are malnourished. This preliminary study profiles the intestinal microbiota of a Risso's dolphin, and provides an additional understanding of the potential relationships between starvation raised by ingesting macro-plastics with cetacean gut microbiota.

Characterization of Antibiotic-Resistant Stenotrophomonas Isolates from Painted Turtles Living in the Wild.

Stenotrophomonas maltophilia is a ubiquitous multidrug-resistant opportunistic pathogen commonly associated with nosocomial infections. The purpose of this study was to isolate and characterize extended-spectrum beta-lactamase (ESBL) producing bacteria from painted turtles (Chrysemys picta) living in the wild and captured in southeastern Wisconsin. Fecal samples from ten turtles were examined for ESBL producing bacteria after incubation on HardyCHROM™ ESBL agar. Two isolates were cultivated and identified by 16S rRNA gene sequencing and whole genome sequencing (WGS) as Stenotrophomonas sp. 9A and S. maltophilia 15A. They were multidrug-resistant, as determined by antibiotic susceptibility testing. Stenotrophomonas sp. 9A was found to produce an extended spectrum beta-lactamase (ESBL) and both isolates were found to be carbapenem-resistant. EDTA-modified carbapenem inactivation method (eCIM) and the modified carbapenem inactivation method (mCIM) tests were used to examine the carbapenemase production and the test results were negative. Through WGS several antimicrobial resistance genes were identified in S. maltophilia 15A. For example a chromosomal L1 ß-lactamase gene, which is known to hydrolyze carbapenems, a L2 ß-lactamase gene, genes for the efflux systems smeABC and smeDEF and the aminoglycosides resistance genes aac(6')-lz and aph(3')-llc were found. An L2 ß-lactamase gene in Stenotrophomonas sp. 9A was identified through WGS.

Revision of total shoulder arthroplasty to hemiarthroplasty: results at mean 5-year follow-up.

BACKGROUND: Although there is a trend to manage failed anatomic total shoulder arthroplasties (aTSA) with revision to a reverse total shoulder arthroplasty, such revisions can be complicated by difficulties in baseplate fixation, instability, and acromial stress fractures. Some cases of failed aTSA may be safely revised to a hemiarthroplasty (HA). The objectives of this study were to report patient-reported outcomes after conversion from aTSA to HA and assess patient and shoulder characteristics associated with a successful outcome. METHODS: Patients who underwent revision from aTSA to HA between 2009 and 2018 were contacted. Patient demographics, surgical history, intraoperative findings, and microbiology results were collected. Patient-reported outcomes were collected with minimum 2-year follow-up. Preoperative radiographic characteristics were reviewed for component positioning and component loosening. Patients with a clinically significant improvement exceeding the minimal clinically important difference (MCID) of the Simple Shoulder Test (SST) were compared with those patients who did not improve past the MCID. RESULTS: Twenty-nine patients underwent conversion from aTSA to HA with a mean follow-up of 4.5 ± 1.8 years. Intraoperative glenoid or humeral component loosening was found in all 29 patients. Pain improved in 25 of 30 patients (87%), and mean pain scores improved from 6.2 ± 2.3 to 3.1 ± 2.4 (P < .001). SST scores improved from 4.1 ± 3.1 to 7.3 ± 3.2 (P < .001), and 18 of 29 patients (62%) had improvement above the SST MCID threshold of 2.4. The mean American Shoulder and Elbow Surgeons score at the latest follow-up was 64 ± 19, and the Single Assessment Numeric Evaluation score was 65 ± 23. Twenty-two of 29 (76%) patients were satisfied with the procedure. Four patients (14%) required conversion to total shoulder arthroplasty-2 to anatomic and 2 to reverse. An additional 3 patients (10%) had a revision HA performed. No significant differences in patient or shoulder characteristics were found in those patients who improved greater than the MCID of the SST compared patients who improved less than the MCID of the SST. Fifty-nine percent of patients had ≥2 positive cultures with the same bacteria, and 82% of these were with Cutibacterium. Seven of 8 patients (88%) with a loose humeral component had ≥2 positive cultures with the same bacteria. DISCUSSION: Component loosening is a common failure mode after aTSA. Revision to HA can improve pain and patient-reported outcomes in most patients.

A Lightweight Remote Sensing Payload for Wildfire Detection and Fire Radiative Power Measurements.

Small uncrewed aerial systems (sUASs) have the potential to serve as ideal platforms for high spatial and temporal resolution wildfire measurements to complement aircraft and satellite observations, but typically have very limited payload capacity. Recognizing the need for improved data from wildfire management and smoke forecasting communities and the potential advantages of sUAS platforms, the Nighttime Fire Observations eXperiment (NightFOX) project was funded by the US National Oceanic and Atmospheric Administration (NOAA) to develop a suite of miniaturized, relatively low-cost scientific instruments for wildfire-related measurements that would satisfy the size, weight and power constraints of a sUAS payload. Here we report on a remote sensing system developed under the NightFOX project that consists of three optical instruments with five individual sensors for wildfire mapping and fire radiative power measurement and a GPS-aided inertial navigation system module for aircraft position and attitude determination. The first instrument consists of two scanning telescopes with infrared (IR) channels using narrow wavelength bands near 1.6 and 4 µm to make fire radiative power measurements with a blackbody equivalent temperature range of 320-1500 °C. The second instrument is a broadband shortwave (0.95-1.7 µm) IR imager for high spatial resolution fire mapping. Both instruments are custom built. The third instrument is a commercial off-the-shelf visible/thermal IR dual camera. The entire system weighs about 1500 g and consumes approximately 15 W of power. The system has been successfully operated for fire observations using a Black Swift Technologies S2 small, fixed-wing UAS for flights over a prescribed grassland burn in Colorado and onboard an NOAA Twin Otter crewed aircraft over several western US wildfires during the 2019 Fire Influence on Regional to Global Environments and Air Quality (FIREX-AQ) field mission.

Combinatorial mutagenesis of rapidly evolving residues yields super-restrictor antiviral proteins.

Antagonistic interactions drive host-virus evolutionary arms races, which often manifest as recurrent amino acid changes (i.e., positive selection) at their protein-protein interaction interfaces. Here, we investigated whether combinatorial mutagenesis of positions under positive selection in a host antiviral protein could enhance its restrictive properties. We tested approximately 700 variants of human MxA, generated by combinatorial mutagenesis, for their ability to restrict Thogotovirus (THOV). We identified MxA super-restrictors with increased binding to the THOV nucleoprotein (NP) target protein and 10-fold higher anti-THOV restriction relative to wild-type human MxA, the most potent naturally occurring anti-THOV restrictor identified. Our findings reveal a means to elicit super-restrictor antiviral proteins by leveraging signatures of positive selection. Although some MxA super-restrictors of THOV were impaired in their restriction of H5N1 influenza A virus (IAV), other super-restrictor variants increased THOV restriction without impairment of IAV restriction. Thus, broadly acting antiviral proteins such as MxA mitigate breadth-versus-specificity trade-offs that could otherwise constrain their adaptive landscape.

Biofilm formation, antimicrobial assay, and toxin-genotypes of Clostridium perfringens type C isolates cultured from a neonatal Yangtze finless porpoise.

This is a culture-dependent study with the objective of pure culturing and characterizing pathogenic bacteria from the blowhole, lung, stomach and fecal samples of a neonatal crucially endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) that died 27 days after birth. Bacteria were inoculated using a swab onto blood and MacConkey agar plates and representative isolates were identified through 16S rRNA gene sequence analysis. A total of three Clostridium perfringens type C strains from the fecal samples were isolated. Toxin genes, including cpa, cpb and cpb2, were detected by PCR amplification, whereas the etx, iap and cpe genes were not detected. Biofilm formation of the three strains was then examined. Only one strain was capable of biofilm formation. In addition, isolates showed strong resistance against the antibiotics amikacin (3/3), erythromycin (1/3), gentamicin (3/3), streptomycin (3/3), and trimethoprim (3/3), while sensitivity to ampicillin (3/3), bacitracin (3/3), erythromycin (2/3), penicillin G (3/3), and tetracycline (3/3). The results suggested C. perfringens type C could have contributed to the death of this neonatal porpoise.

The minimal clinically important differences of the Simple Shoulder Test are different for different arthroplasty types.

BACKGROUND: Preoperative and postoperative patient self-reported measures are the key to understanding the benefit of shoulder arthroplasty for patients with different diagnoses and having different surgical approaches. The minimal clinically important difference (MCID) for patient-reported outcomes such as the Simple Shoulder Test (SST) is often used to document the amount of improvement that is of importance to the patient; however, the MCID may differ for different types of shoulder arthroplasty. The objective of this study was to report the MCID of the SST and the MCID of the percentage of maximal possible improvement (%MPI) for 5 different arthroplasty types. METHODS: Eight hundred eighty-seven patients undergoing shoulder arthroplasty with preoperative SST scores, 2-year postoperative SST scores, and patient satisfaction were included. The sample comprised 368 patients undergoing anatomic total shoulder arthroplasty (aTSA), 330 patients undergoing ream-and-run arthroplasty (R&R), 80 patients undergoing reverse total shoulder arthroplasty (rTSA), 53 patients undergoing cuff tear arthropathy arthroplasty, and 56 patients undergoing hemiarthroplasty. For each type of arthroplasty, the anchor-based method was used for calculating the MCID for both absolute SST scores and %MPI. RESULTS: Significant improvements in SST values were seen for all arthroplasty types. The MCID for SST change was 2.3 overall but ranged from 1.6 for aTSA, to 2.6 for R&R, to 3.7 for rTSA. The MCID for %MPI was 32% overall but ranged from 22% for aTSA to 42% for hemiarthroplasty. The percentage of patients exceeding the MCID threshold was highest for aTSA at 96% and lowest for hemiarthroplasty at 61%. CONCLUSION: The same MCID value may not be appropriate for different types of shoulder arthroplasty. This study reports MCID thresholds that can be used when assessing the effectiveness for each of the common types of shoulder arthroplasty.

Reverse shoulder arthroplasty yields similar results to anatomic total shoulder arthroplasty for the treatment of humeral head avascular necrosis.

BACKGROUND: Avascular necrosis (AVN) of the humeral head frequently results in humeral head collapse and end-stage arthritic changes of the glenohumeral joint. Despite the recent proliferation of reverse total shoulder arthroplasty (RTSA), reports on the use of RTSA for AVN remain limited. The purpose of this study was to document the outcomes of shoulders indicated for RTSA in the setting of humeral head AVN and compare these with AVN shoulders indicated for the gold standard, anatomic total shoulder arthroplasty (aTSA). METHODS: A retrospective review of a multinational shoulder arthroplasty database was performed between August 2005 and August 2017. All shoulders with a preoperative diagnosis of AVN (aTSA in 52 and RTSA in 67) were reviewed. The shoulders in the RTSA cohort were matched (1:1) to shoulders with cuff tear arthropathy, whereas the shoulders in the aTSA cohort were matched (1:1) to shoulders with primary osteoarthritis. The mean follow-up period was 47 months (range, 24-130 months) for RTSA and 54 months (range, 24-124 months) for aTSA. Shoulders were evaluated for active range of motion (ROM) and patient-reported outcome measures (PROMs) prior to surgery and at latest follow-up. Patients treated with RTSA were compared with both the aTSA study cohort and the control group using the Student t test or χ2 test as indicated. RESULTS: RTSAs performed for AVN demonstrated significant improvements in all ROMs and PROMs. Patients undergoing aTSA for AVN were significantly younger than those undergoing RTSA (59 years vs. 73 years, P < .001). At similar follow-up points, the RTSA cohort demonstrated significantly greater improvement in abduction (+51° vs. +32°, P = .03) whereas the aTSA cohort demonstrated significantly greater improvement in internal rotation. Postoperative University of California, Los Angeles scores (30 vs. 27, P = .014) and visual analog scale scores (1.4 vs. 2.4, P = .025) were better after RTSA; however, these differences between prosthesis types did not exceed the minimal clinically important difference. When compared with the control patients, the patients undergoing RTSA for AVN showed similar improvements in all ROMs and PROMs. Similarly, aTSA performed for AVN resulted in comparable improvements in pain, ROMs, and PROMs compared with aTSA performed for primary osteoarthritis. CONCLUSION: RTSA results in similar PROMs to aTSA in the treatment of AVN. Therefore, surgeons should continue to consider other patient factors such as glenoid bone loss and rotator cuff status when selecting implant polarity in patients with AVN.

Macaque interferon-induced transmembrane proteins limit replication of SHIV strains in an Envelope-dependent manner.

HIV-1 does not persistently infect macaques due in part to restriction by several macaque host factors. This has been partially circumvented by generating chimeric SIV/HIV-1 viruses (SHIVs) that encode SIV antagonist of known restriction factors. However, most SHIVs replicate poorly in macaques unless they are further adapted in culture and/or macaques (adapted SHIVs). Therefore, development of SHIVs encoding HIV-1 sequences derived directly from infected humans without adaptation (unadapted SHIVs) has been challenging. In contrast to the adapted SHIVs, the unadapted SHIVs have lower replication kinetics in macaque lymphocytes and are sensitive to type-1 interferon (IFN). The HIV-1 Envelope (Env) in the chimeric virus determines both the reduced replication and the IFN-sensitivity differences. There is limited information on macaque restriction factors that specifically limit replication of the more biologically relevant, unadapted SHIV variants. In order to identify the IFN-induced host factor(s) that could contribute to the inhibition of SHIVs in macaque lymphocytes, we measured IFN-induced gene expression in immortalized pig-tailed macaque (Ptm) lymphocytes using RNA-Seq. We found 147 genes that were significantly upregulated upon IFN treatment in Ptm lymphocytes and 31/147 were identified as genes that encode transmembrane helices and thus are likely present in membranes where interaction with viral Env is plausible. Within this group of upregulated genes with putative membrane-localized proteins, we identified several interferon-induced transmembrane protein (IFITM) genes, including several previously uncharacterized Ptm IFITM3-related genes. An evolutionary genomic analysis of these genes suggests the genes are IFITM3 duplications not found in humans that are both within the IFITM locus and also dispersed elsewhere in the Ptm genome. We observed that Ptm IFITMs are generally packaged at higher levels in unadapted SHIVs when compared to adapted SHIVs. CRISPR/Cas9-mediated knockout of Ptm IFITMs showed that depletion of IFITMs partially rescues the IFN sensitivity of unadapted SHIV. Moreover, we found that the depletion of IFITMs also increased replication of unadapted SHIV in the absence of IFN treatment, suggesting that Ptm IFITMs are likely important host factors that limit replication of unadapted SHIVs. In conclusion, this study shows that Ptm IFITMs selectively restrict replication of unadapted SHIVs. These findings suggest that restriction factors including IFITMs vary in their potency against different SHIV variants and may play a role in selecting for viruses that adapt to species-specific restriction factors.

Reading the tea leaves: Dead transposon copies reveal novel host and transposon biology.

Transposable elements comprise a huge portion of most animal genomes. Unlike many pathogens, these elements leave a mark of their impact via their insertion into host genomes. With proper teasing, these sequences can relay information about the evolutionary history of transposons and their hosts. In a new publication, Larson and colleagues describe a previously unappreciated density of long interspersed element-1 (LINE-1) sequences that have been spliced (LINE-1 and other reverse transcribing elements are necessarily intronless). They provide data to suggest that the retention of these potentially deleterious splice sites in LINE-1 results from the sites' overlap with an important transcription factor binding site. These spliced LINE-1s (i.e., spliced integrated retrotransposed elements [SpiREs]) lose their ability to replicate, suggesting they are evolutionary dead ends. However, the lethality of this splicing could be an efficient means of blocking continued replication of LINE-1. In this way, the record of inactive LINE-1 sequences in the human genome revealed a new, though infrequent, event in the LINE-1 replication cycle and motivates future studies to test whether splicing might be another weapon in the anti-LINE-1 arsenal of host genomes.

Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus.

The African wild dog (AWD) (Lycaon pictus) is a critically endangered species. These animals are hypercarnivores, hunting mostly medium-sized antelope. In this study, using bacterial tag-encoded FLX-Titanium amplicon pyrosequencing (bTEFAP®), the microbiota in the fecal material of AWDs living in the Great Plains Zoo & Delbridge Museum of Natural History was investigated. In both samples, the most predominant bacterial phylum was the Firmicutes with members of the genus Blautia spp. being the most dominant bacteria.

Searching for putative virulence factors in the genomes of Shewanella indica and Shewanella algae.

Bacterial pathogens are a major threat to both humans and animals worldwide. It is crucial to understand the mechanisms of various disease processes at the molecular level. Shewanella species are widespread in the environment and some are considered as emerging opportunistic human and marine mammal pathogens. In this study, putative virulence factors on the genome of Shewanella indica BW, a bacterium isolated from the Bryde's whale (Balaenoptera edeni), were determined. Additionally, for comparative purposes, putative virulence factors from two other S. indica and ten S. algae strains were also determined using the Pathosystems Resource Integration Center (PATRIC) pipeline. We confirmed the presence of previously reported virulence factors and we are proposing several new candidate virulence factors. Interestingly, the putative virulence factors were very similar between the two species with the exception of microbial collagenase which was present in all S. algae genomes, but absent in all S. indica genomes.

Characterization of the Biodiesel Degrading Acinetobacter oleivorans Strain PT8 Isolated from the Fecal Material of a Painted Turtle (Chrysemys picta).

Acinetobacter species are gram-negative, non-fermenting bacteria with coccobacilli morphology. The bacteria are found ubiquitously and have the ability to occupy niches which include environmental sites, animals, and humans. The original purpose of this study was to determine if painted turtles (Chrysemys picta) living in the wild in Western Wisconsin were colonized with carbapenem-resistant bacteria. Fecal samples from ten turtles were examined for carbapenem-resistant bacteria. None of the isolates were found to be carbapenem resistant by antimicrobial susceptibility testing. However, all the isolates were resistant to other ß-lactams and chloramphenicol classes of antimicrobials. One isolate, Acinetobacter oleivorans strain PT8, was selected for additional characterization, including whole-genome sequencing (WGS). Strain PT8 is capable of degrading biodiesel, forming biofilms, and has a putative type 6 gene cluster. Finally, the taxonomic position of the available whole-genome sequences of 25 A. oleivorans genomes from purified isolates was determined.

Reducing roadside runoff: Tillage and compost improve stormwater mitigation in urban soils.

Soils adjacent to urban surfaces are often impaired by construction activities that degrade the natural structure and function of the soil, resulting in altered physical, hydraulic, and vegetative properties that limit the infiltration, storage, and filtration of stormwater runoff. A management approach to enhance the efficacy of vegetated roadside soils for runoff control is the use of compost in conjunction with tillage to improve soil conditions and facilitate improved hydrological function, the establishment of vegetative biomass, and increased nutrient and pollutant attenuation. The purpose of this study was to determine the efficacy of soil improvement measures to reduce runoff volumes and improve water quality along roadsides over time. The effects of tillage with and without compost on 1) bulk density and infiltration rates, 2) runoff volumes, and 3) runoff water quality were evaluated during multiple storm events along two long-established interstate roadsides in North Carolina during 2015 and 2017. Experimental plots were established in the grassed areas adjacent to roads and consisted of an untreated control, tillage only, and tillage amended with compost. Tillage alone did not reduce runoff in roadside soils, however, tillage with compost did improve runoff capture. The patterns in hydrologic performance within and among sites suggests that the incorporation of compost in tilled soils may influence storage potential through different effects on soil properties, such as decreasing bulk density or improving vegetation establishment, thereby increasing evapotranspirative withdrawals, depending on soil texture. Tillage increased sediment concentrations in runoff, however, net export of sediments was reduced with the inclusion of compost due to the reduction of runoff quantities compared to undisturbed areas and tillage alone. Control and treatment plots were equally effective in reducing dissolved nutrient and metal concentrations, however, the improved hydrologic performance in plots with compost decreased net nutrient and metal export in most storms. The results of this study suggest that the incorporation of compost in compacted urban soils may provide significant improvements for biological and physical soil properties that affect stormwater interception and infiltration.