Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria.

BACKGROUND: Mercury (Hg) is highly toxic and has the potential to cause severe health problems for humans and foraging animals when transported into edible plant parts. Soil rhizobia that form symbiosis with legumes may possess mechanisms to prevent heavy metal translocation from roots to shoots in plants by exporting metals from nodules or compartmentalizing metal ions inside nodules. Horizontal gene transfer has potential to confer immediate de novo adaptations to stress. We used comparative genomics of high quality de novo assemblies to identify structural differences in the genomes of nitrogen-fixing rhizobia that were isolated from a mercury (Hg) mine site that show high variation in their tolerance to Hg. RESULTS: Our analyses identified multiple structurally conserved merA homologs in the genomes of Sinorhizobium medicae and Rhizobium leguminosarum but only the strains that possessed a Mer operon exhibited 10-fold increased tolerance to Hg. RNAseq analysis revealed nearly all genes in the Mer operon were significantly up-regulated in response to Hg stress in free-living conditions and in nodules. In both free-living and nodule environments, we found the Hg-tolerant strains with a Mer operon exhibited the fewest number of differentially expressed genes (DEGs) in the genome, indicating a rapid and efficient detoxification of Hg from the cells that reduced general stress responses to the Hg-treatment. Expression changes in S. medicae while in bacteroids showed that both rhizobia strain and host-plant tolerance affected the number of DEGs. Aside from Mer operon genes, nif genes which are involved in nitrogenase activity in S. medicae showed significant up-regulation in the most Hg-tolerant strain while inside the most Hg-accumulating host-plant. Transfer of a plasmid containing the Mer operon from the most tolerant strain to low-tolerant strains resulted in an immediate increase in Hg tolerance, indicating that the Mer operon is able to confer hyper tolerance to Hg. CONCLUSIONS: Mer operons have not been previously reported in nitrogen-fixing rhizobia. This study demonstrates a pivotal role of the Mer operon in effective mercury detoxification and hypertolerance in nitrogen-fixing rhizobia. This finding has major implications not only for soil bioremediation, but also host plants growing in mercury contaminated soils.

SWAN pathway-network identification of common aneuploidy-based oncogenic drivers.

Haploinsufficiency drives Darwinian evolution. Siblings, while alike in many aspects, differ due to monoallelic differences inherited from each parent. In cancer, solid tumors exhibit aneuploid genetics resulting in hundreds to thousands of monoallelic gene-level copy-number alterations (CNAs) in each tumor. Aneuploidy patterns are heterogeneous, posing a challenge to identify drivers in this high-noise genetic environment. Here, we developed Shifted Weighted Annotation Network (SWAN) analysis to assess biology impacted by cumulative monoallelic changes. SWAN enables an integrated pathway-network analysis of CNAs, RNA expression, and mutations via a simple web platform. SWAN is optimized to best prioritize known and novel tumor suppressors and oncogenes, thereby identifying drivers and potential druggable vulnerabilities within cancer CNAs. Protein homeostasis, phospholipid dephosphorylation, and ion transport pathways are commonly suppressed. An atlas of CNA pathways altered in each cancer type is released. These CNA network shifts highlight new, attractive targets to exploit in solid tumors.

Evaluation of Hip Characteristics in Baseball and Softball Athletes with and Without Throwing Arm Pain.

During throwing, the lower extremity assists in the generation and transfer of momentum. Lower extremity stability assists in this transfer by providing a base for distal mobility of the arm segments. This study aimed to determine differences between hip rotational range of motion and strength based on the presence of throwing-arm pain (yes/no) and throwing sport (baseball/softball). We hypothesized those experiencing pain would display decreases in hip range of motion and strength, and that softball players would display greater range of motion than baseball, but less strength based on sex-specific characteristics. Forty-four baseball (13±2 years, 165.2±13.0 cm, 58.5±13.4 kg) and 50 softball players (13±2 years, 160.9±11.2 cm, 62.7±17.9 kg) participated. Multivariate analysis of variance tests (2×2) determined differences in bilateral hip range of motion, total arc of motion, and strength between pain status and sport. There were no significant interactions (>0.05) for pain status and sport on hip range of motion, total arc of motion, and strength. Furthermore, no significant main effects (>0.05) were found for pain status or sport alone on range of motion or strength. Future work should be directed at explaining the effects of hip characteristics on the throwing motion and how it equates to throwing-arm health.

Platelet-Poor versus Platelet-Rich Plasma for the Treatment of Muscle Injuries.

ABSTRACT: Muscle injury in sport results in significant lost time and potential for reinjury for athletes. Autologous blood product, namely, platelet-rich plasma (PRP), has been investigated for possible augmentation of the treatment timeline with prevention of reinjury; however, conflicting results have been identified. A growing body of basic science and clinical literature is forming that supports the use of platelet-poor plasma (PPP) for muscle injury. The purpose of this study was to provide a background of the basic science of PRP versus PPP for muscle injury and to identify and review the clinical evidence for both autologous blood products, including the author's clinical experience utilizing the blood products. At the tissue level, PRP causes myoblast proliferation while PPP has led to myoblast induction, potentially identifying improved native muscle healing. Conflicting studies have been identified for the use of PRP for muscle injury. A growing body of positive results for PPP was identified, but high-quality comparative studies are needed.

Ultrasound-Guided A1 Pulley Release: A Systematic Review.

The purpose of this review was to summarize the current literature pertaining to ultrasound-guided percutaneous A1 pulley release procedures. We searched PubMed, Cochrane Library, Embase, and Web of Science for clinical studies examining ultrasound-guided percutaneous A1 pulley release. A total of 17 studies involving 749 procedures were included in this review. The overall success rate was 97%. There were 23 minor complications (4 cases of hematomas, 15 cases of persistent pain, and 4 cases of transient numbness) and no major complications reported. Ultrasound-guided A1 pulley release is an effective and safe procedure for the treatment of trigger fingers and thumb.

CPP-ACP paste's effect on salivary conditions in patients with removable dentures.

PURPOSE: Older adults with removable dentures experience high rates of both caries (when the natural dentition remains) and salivary gland dysfunction. While many commercial dental therapeutic agents target these two interrelated problems, none have been labeled for use on the fitting surface of removable dentures. Off-label use of MI Paste (GC America, Alsip, IL), a dental therapeutic containing casein-phosphopeptide-amorphous-calcium-phosphate (CPP-ACP), was investigated following its application to the fitting surface of complete denture(s) with subsequent effects on salivary conditions measured. MATERIALS AND METHODS: Salivary flow rate and pH were recorded at baseline and 15 min following the application of 1 mL of CPP-ACP paste to the fitting surface of each participant's denture through whole saliva collection. To assess buffering capacity, equivalent volumes of 0.01 M lactic acid were added to the collected saliva samples, and pH reduction was measured. Comparisons of salivary parameters between baseline and post-CPP-ACP paste application and between subjects with and without self-reported xerostomia were conducted using a paired-sample t-test, Wilcoxon signed-rank test, or two-sample t-test as appropriate. RESULTS: Of the 28 participants (mean age = 70.3 ± 13.7 years, 17 males), 11 reported xerostomia. CPP-ACP-paste application was associated with decreased pH reduction during acid challenge compared to baseline (0.95 ± 0.24 vs. 1.54 ± 0.53, p < 0.001), and a higher final pH following acid challenge (5.93 ± 0.34 vs. 5.40 ± 0.66, p < 0.001). While the flow rates observed at post-CPP-ACP paste application were greater than those at baseline, the difference was not statistically significant (0.67 ± 0.44 mL/min vs. 0.55 ± 0.34 mL/min, p = 0.053). No significant differences were found in any salivary parameters between participants with or without self-reports of xerostomia. CONCLUSIONS: The findings highlight potential positive effects on salivary conditions following the application of the CPP-ACP-containing product, MI Paste, to the fitting surface of a removable complete denture as a potential caries-risk-management tool when natural dentition remains. Determining the caries-preventive clinical significance will require longer-term trials.

Orthobiologic Treatment of Throwing Related Injuries in Sport: A Focused Review of the Published Literature.

ABSTRACT: Because of the growth and development of orthobiologics, in particular platelet-rich plasma, as a potential treatment modality in sports related injuries, it is imperative that providers are aware of the up-to-date published data on the usage of this treatment. While some data are promising, prospective studies are needed to determine the effectiveness of platelet-rich plasma treatment for throwing related injuries. There are limitations with all of the published data that include their retrospective nature, heterogeneity between study designs, and platelet-rich plasma characteristics if reported. While platelet-rich plasma may be used as a likely safe adjuvant to conservative and surgical treatments, prospective randomized controlled studies using appropriately reported platelet-rich plasma concentrations and characteristics will help physicians make more definitive recommendations in regard to platelet-rich plasma treatment. Based on the currently available published data, this treatment may be trialed in the right setting and based on severity and location of injury.

Autophagy modulating therapeutics inhibit ovarian cancer colony generation by polyploid giant cancer cells (PGCCs).

BACKGROUND: Genomic instability and chemoresistance can arise in cancer due to a unique form of plasticity: that of polyploid giant cancer cells (PGCCs). These cells form under the stress of chemotherapy and have higher than diploid chromosome content. PGCCs are able to then repopulate tumors through an asymmetric daughter cell budding process. PGCCs have been observed in ovarian cancer histology, including the deadly and common form high-grade serous ovarian carcinoma (HGSC). We previously discovered that drugs which disrupt the cellular recycling process of autophagy are uniquely efficacious in pre-clinical HGSC models. While autophagy induction has been associated with PGCCs, it has never been previously investigated if autophagy modulation interacts with the PGCC life cycle and this form of tumor cell plasticity. METHODS: CAOV3 and OVCAR3 ovarian cancer cell lines were treated with carboplatin or docetaxel to induce PGCC formation. Microscopy was used to characterize and quantify PGCCs formed by chemotherapy. Two clinically available drugs that inhibit autophagy, hydroxychloroquine and nelfinavir, and a clinically available activator of autophagy, rapamycin, were employed to test the effect of these autophagy modulators on PGCC induction and subsequent colony formation from PGCCs. Crystal violet-stained colony formation assays were used to quantify the tumor-repopulating stage of the PGCC life cycle. RESULTS: Autophagy inhibitors did not prevent PGCC formation in OVCAR3 or CAOV3 cells. Rapamycin did not induce PGCC formation on its own nor did it exacerbate PGCC formation by chemotherapy. However, hydroxychloroquine prevented efficient colony formation in CAOV3 PGCCs induced by carboplatin (27% inhibition) or docetaxel (41% inhibition), as well as in OVCAR3 cells (95% and 77%, respectively). Nelfinavir similarly prevented colony formation in CAOV3 PGCCs induced by carboplatin (64% inhibition) or docetaxel (94% inhibition) as well as in OVCAR3 cells (89% and 80%, respectively). Rapamycin surprisingly also prevented PGCC colony outgrowth (52-84% inhibition). CONCLUSIONS: While the autophagy previously observed to correlate with PGCC formation is unlikely necessary for PGCCs to form, autophagy modulating drugs severely impair the ability of HGSC PGCCs to form colonies. Clinical trials which utilize hydroxychloroquine, nelfinavir, and/or rapamycin after chemotherapy may be of future interest.

Taming the boojum: Being theoretical about peculiarities of learning.

The case of the "biological constraints" movement in mid-20th-century psychology provides a reminder of the weight of psychology's reliance on theory and theory-driven methods. By 1980, a critical mass of demonstrations of the specificity of learning had eroded faith in general-process approaches. A common reaction was to call for a biological orientation. However, this proved not as straightforward as it had seemed, and much of the ostensibly biological research that followed was atheoretical. The successes in this context were due to careful theoretical work by people who appreciated the aims of the involved sciences and the interdependence of the aims with methods. Michael Domjan slowed the field's haphazard rush into ostensible biological research, and rather urged adoption of principled biological approaches. In 1982, his positive recommendation was for comparative psychology to begin to live up to its name, and adopt principled comparative methods as practised in biology. Although lauded, few followed this recommendation. Indeed, even Domjan's own subsequent research was mostly not comparative in the way he had described, but rather involved single species, guided by a behaviour systems approach. With reference to two major perspectives associated with Domjan-comparative methods and behaviour systems theory-I present Domjan's challenge not as being to make our field comparative per se, but to make it theoretical. This challenge remains current.

Asynchronous Online Instruction Leads to Learning Gaps When Compared to a Flipped Classroom.

With the gradual shift to online education models that has taken place in recent decades, research has sought to understand the nuances of student performance in an online model in comparison to more traditional in-person modalities. However, the effects of instructional modality have been difficult to determine given the many variables that exist in course design between these methods. In this study, we attempt to determine the efficacy of asynchronous online instruction by comparing two nearly equivalent courses. The first course was a flipped classroom, a recent and well-studied hybrid model of instruction. The second was an asynchronous fully online course that contained all the same instructional elements as the in-person course but lacked any student or instructor interaction. Student performance was tracked at both a highly-selective private institution and an open-enrollment public institution. Results show that students' performance drops in an asynchronous online course compared to an equivalent in-person experience. Several potential hypotheses are put forth to explain a change in performance that can potentially shape the design of online instruction.

Two-year clinical outcomes of autologous microfragmented adipose tissue in elderly patients with knee osteoarthritis: a multi-centric, international study.

PURPOSE: The aim of this study is to evaluate the outcomes of autologous microfragmented adipose tissue (MFAT) injection in elderly patients with knee osteoarthritis (OA). We hypothesized that MFAT knee infiltration for the treatment of knee OA would yield good clinical results out to two years follow-up. METHODS: Multi-centric, international, open-label study conducted by orthopedic surgery, and/or regenerative medicine facilities utilizing patient registries. Subjects recruited for eligibility. The primary outcome measure was Knee Injury and Osteoarthritis Outcome Score (KOOS). Outcomes and patient factors were compared to baseline, at six, 12, and 24 months. Statistical models were used to assess KOOS subscores and probability of exceeding the Minimally Clinically Important Difference (MCID) or Patient Acceptable Symptom State (PASS), and to assess the effect of the treatment variables on KOOS - Pain. RESULTS: Seventy-five patients, 120 primary treatments, mean age 69.6 years, (95%CI 68.3-70.9), BMI 28.4 (95%CI 27.3-29.6), with KL grade 2 to 4 knee OA treated with a single MFAT injection. KL grades 2 (15.1%), 3 (56.3%), and 4 (28.6%), with 20.8% of knees having previously undergone surgery. Patients with KL grade 2 disease had the best results in KOOS - Pain (P = 0.001), at six, 12, and 24 months. Including advanced KL grade 3 and 4 osteoarthritis patients, significant functional and quality of life success was seen in 106/120 treatments (88.3%, 66 patients) at all follow-up time points. Fourteen treatments (11.7%, 9 patients) failed prior to the study endpoint. CONCLUSION: This study shows that a single-dose MFAT injection leads to clinical, functional, and quality of life improvement at two years in elderly patients, in KL grades 2 to 4 of knee osteoarthritis. These findings provide evidence that this treatment modality could be a safe and effective option to other commonly available treatments in carefully selected patients.

Suggested Curricular Guidelines for Musculoskeletal and Sports Medicine in Physical Medicine and Rehabilitation Residency Training.

ABSTRACT: A sports medicine physician manages musculoskeletal (MSK) injuries and sport-related medical and MSK conditions of patients of all ages and abilities. Physical medicine and rehabilitation physicians (physiatrists) must be adequately trained to provide this care for all patients including, but not limited to, athletes participating in organized sports, the weekend warrior as well as athletes with disabilities. Accreditation Council of Graduate Medical Education core requirements and basic guidelines help physiatry residency training programs develop and implement residency curriculums. The goal of this article is to provide suggested curricular guidelines to optimize physiatrist training in MSK and sports medicine.

Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil.

Members of the bacterial candidate phylum WPS-2 (or Eremiobacterota) are abundant in several dry, bare soil environments. In a bare soil deposited by an extinct iron-sulfur spring, we found that WPS-2 comprised up to 24% of the bacterial community and up to 108 cells per g of soil based on 16S rRNA gene sequencing and quantification. A single genus-level cluster (Ca. Rubrimentiphilum) predominated in bare soils but was less abundant in adjacent forest. Nearly complete genomes of Ca. Rubrimentiphilum were recovered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs). Surprisingly, given the abundance of WPS-2 in bare soils, the genomes did not indicate any capacity for autotrophy, phototrophy, or trace gas metabolism. Instead, they suggest a predominantly aerobic organoheterotrophic lifestyle, perhaps based on scavenging amino acids, nucleotides, and complex oligopeptides, along with lithotrophic capacity on thiosulfate. Network analyses of the entire community showed that some species of Chloroflexi, Actinobacteria, and candidate phylum AD3 (or Dormibacterota) co-occurred with Ca. Rubrimentiphilum and may represent ecological or metabolic partners. We propose that Ca. Rubrimentiphilum act as efficient heterotrophic scavengers. Combined with previous studies, these data suggest that the phylum WPS-2 includes bacteria with diverse metabolic capabilities.

Phosphorylation status of fetuin-A is critical for inhibition of insulin action and is correlated with obesity and insulin resistance.

Fetuin-A (Fet-A), a hepatokine associated with insulin resistance, obesity, and incident type 2 diabetes, is shown to exist in both phosphorylated and dephosphorylated forms in circulation. However, studies on fetuin-A phosphorylation status in insulin-resistant conditions and its functional significance are limited. We demonstrate that serum phosphofetuin-A (Ser312) levels were significantly elevated in high-fat diet-induced obese mice, insulin-resistant Zucker diabetic fatty rats, and in individuals with obesity who are insulin resistant. Unlike serum total fetuin-A, serum phosphofetuin-A was associated with body weight, insulin, and markers of insulin resistance. To characterize potential mechanisms, fetuin-A was purified from Hep3B human hepatoma cells. Hep3B Fet-A was phosphorylated (Ser312) and inhibited insulin-stimulated glucose uptake and glycogen synthesis in L6GLUT4 myoblasts. Furthermore, single (Ser312Ala) and double (Ser312Ala + Ser120Ala) phosphorylation-defective Fet-A mutants were without effect on glucose uptake and glycogen synthesis in L6GLUT4 myoblasts. Together, our studies demonstrate that phosphorylation status of Fet-A (Ser312) is associated with obesity and insulin resistance and raise the possibility that Fet-A phosphorylation may play a role in regulation of insulin action.

The commonly used nonionic surfactant Span 80 has RXRα transactivation activity, which likely increases the obesogenic potential of oil dispersants and food emulsifiers.

Obesity has reached pandemic proportions, and there is mounting evidence that environmental exposures to endocrine disrupting chemicals known as "obesogens" may contribute to obesity and associated medical conditions. The Deepwater Horizon (DWH) oil spill resulted in a massive environmental release of crude oil and remediation efforts applied large quantities of Corexit dispersants to the oil spill. The Corexit-enhanced Water Accommodated Fraction (CWAF) of DWH crude oil contains PPARγ transactivation activity, which is attributed to dioctyl sodium sulfosuccinate (DOSS), a probable obesogen. In addition to its use in oil dispersants, DOSS is commonly used as a stool softener and food additive. Because PPARγ functions as a heterodimer with RXRα to transcriptionally regulate adipogenesis we investigated the potential of CWAF to transactivate RXRα and herein demonstrated that the Corexit component Span 80 has RXRα transactivation activity. Span 80 bound to RXRα in the low micromolar range and promoted adipocyte differentiation of 3T3-L1 preadipocytes. Further, the combination of DOSS and Span 80 increased 3T3-L1 adipocyte differentiation substantially more than treatment with either chemical individually, likely increasing the obesogenic potential of Corexit dispersants. From a public health standpoint, the use of DOSS and Span 80 as food additives heightens concerns regarding their use and mandates further investigations.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.

BACKGROUND: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation. RESULTS: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. CONCLUSIONS: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.

B-lymphocytes support and regulate indirect T-cell alloreactivity in individual patients with chronic antibody-mediated rejection.

We explored how B-lymphocytes influence in vitro T-cell alloresponses in patients with antibody-mediated rejection (AMR), testing whether B-cells would be preferentially involved in this group of patients. Peripheral blood mononuclear cells were collected from 65 patients having biopsy: 14 patients with AMR and 5 with no pathology on protocol; 38 with AMR and 8 with nonimmunologic damage on 'for cause'. Using enzyme-linked immunosorbent spot assays, we found interferon-γ production by indirect allorecognition in 45 of 119 total samples from the 65 patients. B-cells preferentially processed and presented donor alloantigens in samples from AMR patients. In a further 25 samples, B-cell-dependent allo-specific reactivity was shown by depletion of CD25(+) cells and these individuals had higher percentages of CD4CD25hi cells. In 21 samples, reactivity was shown by depletion of CD19(+) cells, associated with polarized cytokine production toward IL-10 after polyclonal activation by IgG/IgM. Overall, this shows a significant contribution by B-cells to indirect donor-specific T-cell reactivity in vitro in patients with AMR. Active suppression by distinct phenotypes of T- or B-cells in approximately half of the patients indicates that chronic AMR is not characterized by a universal loss of immune regulation. Thus, stratified approaches that accommodate the heterogeneity of cell-mediated immunity might be beneficial to treat graft dysfunction.

Vision-based motion capture for the gait analysis of neurodegenerative diseases: A review.

BACKGROUND: Developments in vision-based systems and human pose estimation algorithms have the potential to detect, monitor and intervene early on neurodegenerative diseases through gait analysis. However, the gap between the technology available and actual clinical practice is evident as most clinicians still rely on subjective observational gait analysis or objective marker-based analysis that is time-consuming. RESEARCH QUESTION: This paper aims to examine the main developments of vision-based motion capture and how such advances may be integrated into clinical practice. METHODS: The literature review was conducted in six online databases using Boolean search terms. A commercial system search was also included. A predetermined methodological criterion was then used to assess the quality of the selected articles. RESULTS: A total of seventeen studies were evaluated, with thirteen studies focusing on gait classification systems and four studies on gait measurement systems. Of the gait classification systems, nine studies utilized artificial intelligence-assisted techniques, while four studies employed statistical techniques. The results revealed high correlations of gait features identified by classifier models with existing clinical rating scales. These systems demonstrated generally high classification accuracies and were effective in diagnosing disease severity levels. Gait measurement systems that extract spatiotemporal and kinematic joint information from video data generally found accurate measurements of gait parameters with low mean absolute errors, high intra- and inter-rater reliability. SIGNIFICANCE: Low cost, portable vision-based systems can provide proof of concept for the quantification of gait, expansion of gait assessment tools, remote gait analysis of neurodegenerative diseases and a point of care system for orthotic evaluation. However, certain challenges, including small sample sizes, occlusion risks, and selection bias in training models, need to be addressed. Nevertheless, these systems can serve as complementary tools, equipping clinicians with essential gait information to objectively assess disease severity and tailor personalized treatment for enhanced patient care.