Ossifying fasciitis of the proximal lower extremity.

Ossifying fasciitis is a rare benign tumor of heterotopic bone formation within fascial tissue. We present a case of a 23-year-old female with a nontraumatic painful mass of the left proximal thigh identified as ossifying fasciitis, a lesion that must be considered in the differential diagnosis of soft tissue tumors.

The effects of torula yeast as a protein source on apparent total tract digestibility, inflammatory markers, and fecal microbiota dysbiosis index in Labrador Retrievers with chronically poor stool quality.

This study examined the effects of varying protein sources on apparent total tract digestibility, inflammatory markers, and fecal microbiota in Labrador Retrievers with historically poor stool quality. Thirty dogs (15 male, 15 female; aged 0.93 to 11.7 yr) with stool quality scores ≤2.5 on a 5-point scale (1 representing liquid stool and 5 representing firm stool) were randomly assigned to 1 of 3 nutritionally complete diets with differing protein sources and similar macronutrient profiles: 1) chicken meal (n = 10); 2) 10% brewer's yeast (n = 10); or 3) 10% torula yeast (n = 10). Another 10 dogs (five male, five female) with normal stool quality (scores ranging from 3 to 4) received diet 1 and served as negative control (NC). All dogs were fed diet 1 for 7 days, then provided their assigned treatment diets from days 7 to 37. Daily stool scores and weekly body weights were recorded. On days 7, 21, and 36, blood serum was analyzed for c-reactive protein (CRP), and feces for calgranulin C (S100A12), α1-proteinase inhibitor (α1-PI), calprotectin, and microbiota dysbiosis index. Apparent total tract digestibility was assessed using the indicator method with 2 g titanium dioxide administered via oral capsules. Stool scores were greater in NC (P < 0.01) as designed but not affected by treatment × time interaction (P = 0.64). Body weight was greater (P = 0.01) and CRP lower (P < 0.01) in NC dogs. Dry matter and nitrogen-free extract digestibility did not differ among groups (P ≥ 0.14). Negative controls had greater fat digestibility compared to BY (94.64 ±â€…1.33% vs. 91.65 ±â€…1.25%; P = 0.02). The overall effect of treatment was significant for protein digestibility (P = 0.03), but there were no differences in individual post hoc comparisons (P ≥ 0.07). Treatment did not affect S100A12 or α1-PI (P ≥ 0.44). Calprotectin decreased at a greater rate over time in TY (P < 0.01). The dysbiosis index score for BY and TY fluctuated less over time (P = 0.01). Blautia (P = 0.03) and Clostridium hiranonis (P = 0.05) abundances were reduced in BY and TY. Dogs with chronically poor stool quality experienced reduced body weights and increased serum CRP, but TY numerically increased protein digestibility, altered the microbiome, and reduced fecal calprotectin. Torula yeast is a suitable alternative protein source in extruded canine diets, but further research is needed to understand the long-term potential for improving the plane of nutrition and modulating gut health.

Pet and human populations continue to grow and compete for nutritious, sustainable protein sources. The incorporation of alternative proteins like torula yeast can provide a solution to this problem. Torula yeast also may have additional health benefits like reducing gut inflammation. To test its effects in dogs, we fed Labrador Retrievers with chronically poor stool quality either a control diet with chicken meal, a diet with 10% brewer's yeast, or a diet with 10% torula yeast. We compared their responses to dogs with normal stool quality fed the control diet. Dogs with chronically poor stool quality had lower body weights and increased systemic inflammation compared to those with good stool quality. Calprotectin, a marker of gut inflammation, was reduced more in dogs fed torula yeast than in dogs fed chicken meal. Torula and brewer's yeast also changed the abundance of certain gut bacteria. Torula yeast may be added to dog diets with no negative effects and can alter the gut environment in Labrador Retrievers with chronically poor stool quality.

Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.

Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 yr; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (N = 18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment × transport were tested, with P < 0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet × transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.

The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of dogs supplemented with a Saccharomyces cerevisiae fermentation product (SCFP) and subjected to transport stress. Thirty-six adult dogs were randomly assigned to a control diet or an SCFP-supplemented diet (N = 18 per group) and fed for 11 wk. At that time, a transport stress challenge was conducted. Fresh fecal samples were collected for measurement of general characteristics, microbiota, and metabolites before and after transport stress. Transport stress increased fecal indoles and Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium populations and decreased fecal Fusobacteria, Streptococcus, and Fusobacterium populations. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone, but several diet × transport interactions were significant. Following transport, fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. Fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs. SCFP supplementation may provide benefits to dogs undergoing stress, but proper dosages need to be determined.

The inhibitor of κB kinase ß (IKKß) phosphorylates IκBα twice in a single binding event through a sequential mechanism.

Phosphorylation of Inhibitor of κB (IκB) proteins by IκB Kinase ß (IKKß) leads to IκB degradation and subsequent activation of nuclear factor κB transcription factors. Of particular interest is the IKKß-catalyzed phosphorylation of IκBα residues Ser32 and Ser36 within a conserved destruction box motif. To investigate the catalytic mechanism of IKKß, we performed pre-steady-state kinetic analysis of the phosphorylation of IκBα protein substrates catalyzed by constitutively active, human IKKß. Phosphorylation of full-length IκBα catalyzed by IKKß was characterized by a fast exponential phase followed by a slower linear phase. The maximum observed rate (kp) of IKKß-catalyzed phosphorylation of IκBα was 0.32 s-1 and the binding affinity of ATP for the IKKß•IκBα complex (Kd) was 12 µM. Substitution of either Ser32 or Ser36 with Ala, Asp, or Cys reduced the amplitude of the exponential phase by approximately 2-fold. Thus, the exponential phase was attributed to phosphorylation of IκBα at Ser32 and Ser36, whereas the slower linear phase was attributed to phosphorylation of other residues. Interestingly, the exponential rate of phosphorylation of the IκBα(S32D) phosphomimetic amino acid substitution mutant was nearly twice that of WT IκBα and 4-fold faster than any of the other IκBα amino acid substitution mutants, suggesting that phosphorylation of Ser32 increases the phosphorylation rate of Ser36. These conclusions were supported by parallel experiments using GST-IκBα(1-54) fusion protein substrates bearing the first 54 residues of IκBα. Our data suggest a model wherein, IKKß phosphorylates IκBα at Ser32 followed by Ser36 within a single binding event.

Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs subjected to exercise challenge.

The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of dogs fed a Saccharomyces cerevisiae fermentation product (SCFP) and subjected to exercise challenge in untrained and trained states. Thirty-six adult dogs (18 male, 18 female; mean age: 7.1 yr; mean body weight: 29.0 kg) were randomly assigned to control or SCFP-supplemented (250 mg/dog/d) diets and fed for 10 wk. After 3 wk, dogs were given an exercise challenge (6.5 km run), with fresh fecal samples collected pre- and post-challenge. Dogs were then trained by a series of distance-defined running exercise regimens over 7 wk (two 6.4 km runs/wk for 2 wk; two 9.7 km runs/wk for 2 wk; two 12.9 km runs/wk for 2 wk; two 3.2 km runs/wk). Dogs were then given exercise challenge (16 km run) in the trained state, with fresh fecal samples collected pre- and post-challenge. Fecal microbiota data were evaluated using QIIME2, while all other data were analyzed using the Mixed Models procedure of SAS. Effects of diet, exercise, and diet*exercise were tested with P < 0.05 considered significant. Exercise challenge reduced fecal pH and ammonia in both treatments, and in untrained and trained dogs. After the exercise challenge in untrained dogs, fecal indole, isobutyrate, and isovalerate were reduced, while acetate and propionate were increased. Following the exercise challenge in trained dogs, fecal scores and butyrate decreased, while isobutyrate and isovalerate increased. SCFP did not affect fecal scores, pH, dry matter, or metabolites, but fecal Clostridium was higher in controls than in SCFP-fed dogs over time. SCFP and exercise challenge had no effect on alpha or beta diversity in untrained dogs. However, the weighted principal coordinate analysis plot revealed clustering of dogs before and after exercise in trained dogs. After exercise challenge, fecal Collinsella, Slackia, Blautia, Ruminococcus, and Catenibacterium were higher and Bacteroides, Parabacteroides, Prevotella, Phascolarctobacterium, Fusobacterium, and Sutterella were lower in both untrained and trained dogs. Using qPCR, SCFP increased fecal Turicibacter, and tended to increase fecal Lactobacillus vs. controls. Exercise challenge increased fecal Turicibacter and Blautia in both untrained and trained dogs. Our findings show that exercise and SCFP may affect the fecal microbiota of dogs. Exercise was the primary cause of the shifts, however, with trained dogs having more profound changes than untrained dogs.

The objective of this study was to determine the fecal characteristics, microbiota, and metabolites of dogs fed a Saccharomyces cerevisiae fermentation product (SCFP) and subjected to exercise challenge in untrained and trained states. Thirty-six adult dogs were randomly assigned to control or SCFP-supplemented (250 mg/d) diets and fed for 10 wk. An exercise challenge was administered while dogs were in an untrained state and a trained state (after 7 wk of an exercise regimen), with fresh fecal samples collected pre- and post-challenge. Exercise challenge reduced fecal pH and ammonia in all dogs. After the exercise challenge in untrained dogs, fecal indole, isobutyrate, and isovalerate concentrations were reduced, while acetate and propionate concentrations were increased. Following exercise challenge in trained dogs, fecal scores and butyrate concentrations decreased, while isobutyrate and isovalerate increased. SCFP reduced fecal Clostridium over time vs. controls. Beta diversity analysis revealed clustering of dogs before and after exercise in trained dogs. After exercise challenge, over 10 bacterial genera were altered in untrained and trained dogs. Our findings show that exercise and SCFP may affect the fecal microbiota of dogs, but exercise was the primary cause of the shifts and trained dogs had more profound changes than untrained dogs.

Impact of supplemented undenatured type II collagen on pain and mobility in healthy Labrador Retrievers during an exercise regimen.

The aim of this experiment was to evaluate the effect of undenatured type II collagen supplementation on inflammation and pain using gait analysis and industry-accepted pain and mobility questionnaires during an exercise regimen in healthy dogs. Forty healthy Labrador Retrievers (20 male/20 female; range: 5 to 12 yr) were sorted into two groups: undenatured type II collagen group receiving 40 mg UC-II product (10 mg total collagen and ≥3% undenatured type II collagen) and placebo group receiving 40 mg maltodextrin daily by capsule. After 2 wk loading, all dogs began an 11 wk endurance exercise regimen consisting of two weekly runs, starting at 5 km and increasingly incrementally to 8 km, with one final 16 km run. Gait analysis was performed at baseline; before, 24 and 48 h after the first 5 km run; and before, 24 and 48 h after the final 16 km run. Gait analysis was calculated to obtain a Four Rivers Kennel (FRK) Inflammation Index score. Dogs were scored according to the Liverpool Osteoarthritis in Dogs (LOAD) and Canine Brief Pain Inventory (CBPI) assessments at baseline, before and after the first 5 km run, and before and after the final 16 km run. On the LOAD questionnaire, undenatured type II collagen group had improved "how active is the dog" (P = 0.03) and less "stiffness after a lie down" (P = 0.041) compared with placebo at pre 5 km. Undenatured type II collagen appeared to mitigate the development of pain after exercise compared with placebo, as related to the CPBI assessment. Undenatured type II collagen dogs had lower "pain at worst" pre 5 km (P = 0.021), "pain at least" post 5 km (P = 0.015), "pain at average" post 5 km (P = 0.046), and "pain as it is now" post 16 km (P = 0.006) compared with placebo dogs. Undenatured type II collagen was more effective than placebo at mitigating inflammation on gait analysis per the FRK Inflammation Index. Undenatured type II collagen dogs had a 6.42 lower FRK Inflammation Index score at 24 h post 5 km (P = 0.032) and 6.3 lower score at 24 h post 16 km (P = 0.029), indicating the mitigation of inflammation on gait analysis. When considering the change between timepoints, undenatured type II collagen had a lower increase in FRK Inflammation scores compared with placebo for baseline to pre 5 km (P < 0.001), pre 16 km to 24 h post 16 km (P = 0.028), and pre 16 km to 48 h post 16 km (P = 0.027). Undenatured type II collagen supplemented Labrador Retrievers improved pain assessment variables and improved FRK Inflammation Index on gait analysis.

L-Carnitine metabolism, protein turnover and energy expenditure in supplemented and exercised Labrador Retrievers.

L-Carnitine is critical for protection against bioaccumulation, long-chain fatty acid transportation and energy production. Energy production becomes important as the body maintains lean mass, repairs muscles and recovers from oxidative stress. The aim was to investigate the effects of supplemented L-carnitine on protein turnover (PT), energy expenditure (EE) and carnitine metabolism in muscle/serum of Labrador Retrievers. In a series of experiments, all dogs were fed a low-carnitine diet and sorted into one of two groups: L-carnitine (LC) supplemented daily with 125 mg L-carnitine and 3.75 g sucrose or placebo (P) supplemented with 4 g sucrose daily. The experiments consisted of analyses of muscle/serum for L-carnitine content (EXP1), a protein turnover experiment (EXP2) and analysis of substrate utilization via indirect calorimetry (EXP3). EXP1: 20 Labradors (10 M/10 F) performed a 13 week running regimen. L-Carnitine content was analysed in the serum and biceps femoris muscle before/after a 24.1 km run. LC serum had higher total (p < .001; p = .001), free (p < .001; p = .001) and esterified (p = .001; p = .003) L-carnitine pre- and post-run respectively. LC muscle had significantly higher free L-carnitine post-run (p = .034). EXP2: 26 Labs (13 M/13 F) performed a 60-day running regimen. For the final run, half of the Labradors from each treatment rested and half ran 24.1 km. Twenty-four Labradors received isotope infusion, and then, a biopsy of the biceps femoris of all 26 Labradors was taken to determine PT. Resting/exercised LC had a lower fractional breakdown rate (FBR) versus P group (p = .042). LC females had a lower FBR v. P females (p = .046). EXP3: Respiration of 16 Labradors (8 M/8 F) was measured via indirect calorimetry over 15 week. All dogs ran on a treadmill for 30 min at 30% VO2 max (6.5 kph), resulting in higher maximum and mean EE in LC females v. P females (p = .021; p = .035). Implications for theory, practice and future research are discussed.

Clinical Practice Guideline: Evaluation of the Neck Mass in Adults.

Objective Neck masses are common in adults, but often the underlying etiology is not easily identifiable. While infections cause most of the neck masses in children, most persistent neck masses in adults are neoplasms. Malignant neoplasms far exceed any other etiology of adult neck mass. Importantly, an asymptomatic neck mass may be the initial or only clinically apparent manifestation of head and neck cancer, such as squamous cell carcinoma (HNSCC), lymphoma, thyroid, or salivary gland cancer. Evidence suggests that a neck mass in the adult patient should be considered malignant until proven otherwise. Timely diagnosis of a neck mass due to metastatic HNSCC is paramount because delayed diagnosis directly affects tumor stage and worsens prognosis. Unfortunately, despite substantial advances in testing modalities over the last few decades, diagnostic delays are common. Currently, there is only 1 evidence-based clinical practice guideline to assist clinicians in evaluating an adult with a neck mass. Additionally, much of the available information is fragmented, disorganized, or focused on specific etiologies. In addition, although there is literature related to the diagnostic accuracy of individual tests, there is little guidance about rational sequencing of tests in the course of clinical care. This guideline strives to bring a coherent, evidence-based, multidisciplinary perspective to the evaluation of the neck mass with the intention to facilitate prompt diagnosis and enhance patient outcomes. Purpose The primary purpose of this guideline is to promote the efficient, effective, and accurate diagnostic workup of neck masses to ensure that adults with potentially malignant disease receive prompt diagnosis and intervention to optimize outcomes. Specific goals include reducing delays in diagnosis of HNSCC; promoting appropriate testing, including imaging, pathologic evaluation, and empiric medical therapies; reducing inappropriate testing; and promoting appropriate physical examination when cancer is suspected. The target patient for this guideline is anyone ≥18 years old with a neck mass. The target clinician for this guideline is anyone who may be the first clinician whom a patient with a neck mass encounters. This includes clinicians in primary care, dentistry, and emergency medicine, as well as pathologists and radiologists who have a role in diagnosing neck masses. This guideline does not apply to children. This guideline addresses the initial broad differential diagnosis of a neck mass in an adult. However, the intention is only to assist the clinician with a basic understanding of the broad array of possible entities. The intention is not to direct management of a neck mass known to originate from thyroid, salivary gland, mandibular, or dental pathology as management recommendations for these etiologies already exist. This guideline also does not address the subsequent management of specific pathologic entities, as treatment recommendations for benign and malignant neck masses can be found elsewhere. Instead, this guideline is restricted to addressing the appropriate work-up of an adult patient with a neck mass that may be malignant in order to expedite diagnosis and referral to a head and neck cancer specialist. The Guideline Development Group sought to craft a set of actionable statements relevant to diagnostic decisions made by a clinician in the workup of an adult patient with a neck mass. Furthermore, where possible, the Guideline Development Group incorporated evidence to promote high-quality and cost-effective care. Action Statements The development group made a strong recommendation that clinicians should order a neck computed tomography (or magnetic resonance imaging) with contrast for patients with a neck mass deemed at increased risk for malignancy. The development group made the following recommendations: (1) Clinicians should identify patients with a neck mass who are at increased risk for malignancy because the patient lacks a history of infectious etiology and the mass has been present for ≥2 weeks without significant fluctuation or the mass is of uncertain duration. (2) Clinicians should identify patients with a neck mass who are at increased risk for malignancy based on ≥1 of these physical examination characteristics: fixation to adjacent tissues, firm consistency, size >1.5 cm, or ulceration of overlying skin. (3) Clinicians should conduct an initial history and physical examination for patients with a neck mass to identify those with other suspicious findings that represent an increased risk for malignancy. (4) For patients with a neck mass who are not at increased risk for malignancy, clinicians or their designees should advise patients of criteria that would trigger the need for additional evaluation. Clinicians or their designees should also document a plan for follow-up to assess resolution or final diagnosis. (5) For patients with a neck mass who are deemed at increased risk for malignancy, clinicians or their designees should explain to the patient the significance of being at increased risk and explain any recommended diagnostic tests. (6) Clinicians should perform, or refer the patient to a clinician who can perform, a targeted physical examination (including visualizing the mucosa of the larynx, base of tongue, and pharynx) for patients with a neck mass deemed at increased risk for malignancy. (7) Clinicians should perform fine-needle aspiration (FNA) instead of open biopsy, or refer the patient to someone who can perform FNA, for patients with a neck mass deemed at increased risk for malignancy when the diagnosis of the neck mass remains uncertain. (8) For patients with a neck mass deemed at increased risk for malignancy, clinicians should continue evaluation of patients with a cystic neck mass, as determined by FNA or imaging studies, until a diagnosis is obtained and should not assume that the mass is benign. (9) Clinicians should obtain additional ancillary tests based on the patient's history and physical examination when a patient with a neck mass is deemed at increased risk for malignancy who does not have a diagnosis after FNA and imaging. (10) Clinicians should recommend evaluation of the upper aerodigestive tract under anesthesia, before open biopsy, for patients with a neck mass deemed at increased risk for malignancy and without a diagnosis or primary site identified with FNA, imaging, and/or ancillary tests. The development group recommended against clinicians routinely prescribing antibiotic therapy for patients with a neck mass unless there are signs and symptoms of bacterial infection.

Clinical Practice Guideline: Evaluation of the Neck Mass in Adults Executive Summary.

The American Academy of Otolaryngology-Head and Neck Surgery Foundation has published a supplement to this issue of Otolaryngology-Head and Neck Surgery featuring the "Clinical Practice Guideline: Evaluation of the Neck Mass in Adults." To assist in implementing the guideline recommendations, this article summarizes the rationale, purpose, and key action statements. The 12 recommendations developed emphasize reducing delays in diagnosis of head and neck squamous cell carcinoma; promoting appropriate testing, including imaging, pathologic evaluation, and empiric medical therapies; reducing inappropriate testing; and promoting appropriate physical examination when cancer is suspected.

Silicone breast implant rupture: a review.

Silicone breast implants have been in use for nearly 6 decades. In this time they have undergone significant changes in design and use. They have been subject to intense scrutiny with regard to safety and efficacy, including an almost 10 years moratorium on their use. The current generations of implants have been followed via the manufacturer's Core studies in order to obtain long term data regarding safety and complications. The results of the more recent studies are compiled in this review. Rupture rates are initially very low and begin to increase after 6-8 years of implantation. Implant rupture may be detected by physical exam, ultrasound or magnetic resonance imaging (MRI). The majority of silicone implant ruptures are clinically undetectable. Symptomatic patients may present with capsular contracture, breast lumps or changes in breast shape. The most common cause of implant rupture is instrument damage during placement. Implant rupture may be confined to the peri-prosthetic capsule or may extravasate into the breast tissue. Patients with ruptured implants have been studied closely and the consensus of the literature states there are no health risks associated with implant rupture. Symptomatic patients with ruptured implants should be offered the choice of observation, or explantation and capsulectomy with or without replacement.

Backbone assignment of the binary complex of the full length Sulfolobus solfataricus DNA polymerase IV and DNA.

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several ß-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes.

Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.

Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180° with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.

Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex.

Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.

Identification of an unfolding intermediate for a DNA lesion bypass polymerase.

Sulfolobus solfataricus DNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C.

Presteady state kinetic investigation of the incorporation of anti-hepatitis B nucleotide analogues catalyzed by noncanonical human DNA polymerases.

Antiviral nucleoside analogues have been developed to inhibit the enzymatic activities of the hepatitis B virus (HBV) polymerase, thereby preventing the replication and production of HBV. However, the usage of these analogues can be limited by drug toxicity because the 5'-triphosphates of these nucleoside analogues (nucleotide analogues) are potential substrates for human DNA polymerases to incorporate into host DNA. Although they are poor substrates for human replicative DNA polymerases, it remains to be established whether these nucleotide analogues are substrates for the recently discovered human X- and Y-family DNA polymerases. Using presteady state kinetic techniques, we have measured the substrate specificity values for human DNA polymerases ß, λ, η, ι, κ, and Rev1 incorporating the active forms of the following anti-HBV nucleoside analogues approved for clinical use: adefovir, tenofovir, lamivudine, telbivudine, and entecavir. Compared to the incorporation of a natural nucleotide, most of the nucleotide analogues were incorporated less efficiently (2 to >122,000) by the six human DNA polymerases. In addition, the potential for entecavir and telbivudine, two drugs which possess a 3'-hydroxyl, to become embedded into human DNA was examined by primer extension and DNA ligation assays. These results suggested that telbivudine functions as a chain terminator, while entecavir was efficiently extended by the six enzymes and was a substrate for human DNA ligase I. Our findings suggested that incorporation of anti-HBV nucleotide analogues catalyzed by human X- and Y-family polymerases may contribute to clinical toxicity.

Backbone assignment of the little finger domain of a Y-family DNA polymerase.

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and ß carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases.

Higher eukaryotes encode various Y-family DNA polymerases to perform global DNA lesion bypass. To provide complete mutation spectra for abasic lesion bypass, we employed short oligonucleotide sequencing assays to determine the sequences of abasic lesion bypass products synthesized by human Y-family DNA polymerases eta (hPolη), iota (hPolι) and kappa (hPolκ). The fourth human Y-family DNA polymerase, Rev1, failed to generate full-length lesion bypass products after 3 h. The results indicate that hPolι generates mutations with a frequency from 10 to 80% during each nucleotide incorporation event. In contrast, hPolη is the least error prone, generating the fewest mutations in the vicinity of the abasic lesion and inserting dAMP with a frequency of 67% opposite the abasic site. While the error frequency of hPolκ is intermediate to those of hPolη and hPolι, hPolκ has the highest potential to create frameshift mutations opposite the abasic site. Moreover, the time (t(50)(bypass)) required to bypass 50% of the abasic lesions encountered by hPolη, hPolι and hPolκ was 4.6, 112 and 1 823 s, respectively. These t(50)(bypass) values indicate that, among the enzymes, hPolη has the highest abasic lesion bypass efficiency. Together, our data suggest that hPolη is best suited to perform abasic lesion bypass in vivo.