TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs.

T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

Geochemistry of apollo 15 basalt 15555 and soil 15531.

Major and trace element concentrations have been determined by atomic absorption spectrophotometry, colorimetry, and isotope dilution in Apollo 15 mare basalt 15555 from the Hadley Rille area; trace element concentrations have also been determined in plagioclase and pyroxene separates from basalt 15555 and in soil 15531 from the same area. Basalt 15555 most closely resembles in composition the Apollo 12 olivine-rich basalts. The concentrations of lithium, potassium, rubidium, barium, rare-earth elements, and zirconium in basalt 15555 are the lowest, and the negative europium anomaly is the smallest, reported for lunar basalts; this basalt might be the least differentiated material yet returned from the moon. Crystallization and removal of about 6 percent of plagioclase similar to that contained in the basalt would account for the observed europium anomaly; if plagioclase is not on the liquidus of this basalt, a multistage origin is indicated. Mineral data indicate that plagioclase and pyroxene approached quasi-equilibrium. Most of the chemical differences between basalt 15555 and soil 15531 would be accounted for if the soil were a mixture of 88 percent basalt, 6 percent KREEP (a component, identified in other Apollo soils, rich in potassium, rare-earth elements, and phosphorus) and 6 percent plagioclase (anorthosite?).

Role of timing in assessment of nerve regeneration.

Small animal models are indispensable for research on nerve injury and reconstruction, but their superlative regenerative potential may confound experimental interpretation. This study investigated time-dependent neuroregenerative phenomena in rodents. Forty-six Lewis rats were randomized to three nerve allograft groups treated with 2 mg/(kg day) tacrolimus; 5 mg/(kg day) Cyclosporine A; or placebo injection. Nerves were subjected to histomorphometric and walking track analysis at serial time points. Tacrolimus increased fiber density, percent neural tissue, and nerve fiber count and accelerated functional recovery at 40 days, but these differences were undetectable by 70 days. Serial walking track analysis showed a similar pattern of recovery. A "blow-through" effect is observed in rodents whereby an advancing nerve front overcomes an experimental defect given sufficient time, rendering experimental groups indistinguishable at late time points. Selection of validated time points and corroboration in higher animal models are essential prerequisites for the clinical application of basic research on nerve regeneration.

Binary imaging analysis for comprehensive quantitative histomorphometry of peripheral nerve.

Quantitative histomorphometry is the current gold standard for objective measurement of nerve architecture and its components. Many methods still in use rely heavily upon manual techniques that are prohibitively time consuming, predisposing to operator fatigue, sampling error, and overall limited reproducibility. More recently, investigators have attempted to combine the speed of automated morphometry with the accuracy of manual and semi-automated methods. Systematic refinements in binary imaging analysis techniques combined with an algorithmic approach allow for more exhaustive characterization of nerve parameters in the surgically relevant injury paradigms of regeneration following crush, transection, and nerve gap injuries. The binary imaging method introduced here uses multiple bitplanes to achieve reproducible, high throughput quantitative assessment of peripheral nerve. Number of myelinated axons, myelinated fiber diameter, myelin thickness, fiber distributions, myelinated fiber density, and neural debris can be quantitatively evaluated with stratification of raw data by nerve component. Results of this semi-automated method are validated by comparing values against those obtained with manual techniques. The use of this approach results in more rapid, accurate, and complete assessment of myelinated axons than manual techniques.

Mechanical evaluation of bone samples following alendronate therapy in healthy male dogs.

Alendronate and other bisphosphonates are clinically efficacious in treating postmenopausal osteoporosis, Paget's disease and hypercalcemia associated with malignancy. Because bisphosphonates are being considered for use in younger patients with joint replacements to prevent osteolysis, and for stress fracture prophylaxis in military recruits, it is important to know how bisphosphonate therapy affects healthy bone. We sought to determine whether bones from healthy male dogs exhibit alterations in structural or mechanical properties following alendronate treatment for 23 weeks. We tested trabecular tissue samples in compression and determined tissue ash density. We tested whole long bones in bending and torsion. For trabecular samples, we evaluated trabecular modulus, strength, and density. For whole bone specimens, we compared structural stiffness and ultimate load. We found no significant differences in any measure, between canines treated with alendronate for 23 weeks and controls, although we found consistent trends toward higher properties in the treated group. Correlation analysis revealed significant relationships between stiffness and strength measures for each mechanical test. Our results indicate bisphosphonate treatment in healthy canines does not weaken the properties of bone. The trends indicate a slight positive overall effect of alendronate treatment on the mechanical properties of healthy canine bone.

FK506 and anti-CD40 ligand in peripheral nerve allotransplantation.

PURPOSE: Immunomodulatory agents are often combined in organ transplantation to minimize toxicity and enhance therapeutic effect. We hypothesized that combining low-dose FK506 with anti-CD40 Ligand (anti-CD40L mAb) would enhance regeneration through peripheral nerve allografts while preserving immune unresponsiveness. METHODS: Eighty Balb/cJ mice underwent tibial nerve grafting and were randomized to 10 groups treated with combinations of anti-CD40L mAb therapy, low-dose FK506 (0.5 mg/kg/day), high-dose FK506 (2 mg/kg/day), and high-dose cyclosporine (25 mg/kg/day). At 3 weeks, histomorphometry and cytokine secretion assays were performed. RESULTS: Animals receiving low-dose FK506 with anti-CD40L mAb exhibited robust nerve regeneration comparable to the isograft and high-dose FK506 allograft groups. Nerve density was significantly increased in the low-dose FK506 with anti-CD40L mAb group compared to animals receiving anti-CD40L mAb alone (p < 0.05). Combining anti-CD40L mAb with high dose cyclosporine decreased nerve fiber counts, nerve density, and percent nerve (p < 0.05). Interferon-gamma production was markedly elevated in untreated allografts compared to all other treatment groups (p < 0.05). Cytokine secretion was intermediate in the low-dose FK506 alone group and suppressed in all remaining groups. CONCLUSION: When combined with anti-CD40L mAb, low-dose FK506 enhances nerve regeneration without disrupting immune unresponsiveness.

Long-term limb allograft survival using anti-CD40L antibody in a murine model.

BACKGROUND: Costimulation blockade has been shown to be effective in achieving donor-specific immune unresponsiveness in models of organ transplantation. This study represents the first application of blockade of the CD40 costimulatory pathway to a murine model of limb allotransplantation. METHODS: Eighteen Balb/c mice (H-2K(d)) were randomized to four groups. The control group (n=5) received syngeneic limb transplants from Balb/c donors. The experimental groups were recipients of limb allografts from C57Bl/6 mice (H-2K(b)) and received either no treatment (n=5) or treatment with MR1 (hamster antimouse CD40 ligand monoclonal antibody) 500 microg intraperitoneally (IP) on days 0, 2, 4, 6, 14, 28, and 60 (n=5). A fourth group received myocutaneous allografts from C57Bl/6 donors and the same treatment with MR1 (n=5). RESULTS: Untreated limb allografts were rejected at a mean of 9.6+/-1.1 days postoperatively. MR1-treated limb allografts underwent rejection of the skin component at a mean of 75+/-25 days whereas the musculoskeletal component survived to a mean of 222+/-84 days with two allografts surviving more than 10 months (P<0.001). The MR1-treated myocutaneous allografts were rejected after 16.2+/-2 days. All groups demonstrated acute rejection on histology except the treated limb allograft group, which was more suggestive of a chronic process. No chimerism was detected in this group by flow cytometry. CONCLUSIONS: CD40 costimulatory blockade significantly prolonged limb-allograft survival, and the bone-marrow component may have played an important role. Tolerance was not achieved, and histologic evaluation suggested chronic rejection as a possible cause of allograft loss.

Brachial plexus injuries.

Severe trauma to the brachial plexus most often occurs in young adult men and is a crippling injury that requires management in a timely fashion for optimal functional recovery and pain control. The surgical management of such injuries is well established, and the techniques continue to evolve. Current management options consist of primary repair in the acute setting, neurolysis, neuroma resection and nerve grafting, motor and sensory nerve transfers, and muscle and tendon transfers. Shoulder andwrist fusion can also play a role in the overall management of these patients. The best operative plan varies depending on the patient's level and extent of injury and the surgeon's preference and experience. The pre- and postoperative care of these patients is ideally managed by a team that has experience with such problems, including personnel knowledgeable in their postoperative rehabilitation. The total reconstructive process generally consists of more than one operation, and the postoperative rehabilitation is long and intensive. Nevertheless, with a highly motivated patient and a dedicated and specialized surgical team, the prognosis for functional recovery is good, and these patients can still lead productive and satisfying lives.

Parasitic and phoretic arthropods of the elephant-eared and the Santa Cruz kangaroo rats.

The parasitic and phoretic arthropods of the elephant-eared kangaroo rat (Dipodomys elephantinus) and Santa Cruz kangaroo rat (D. venustus) are reported; most of these represent new host records. Thirteen of 14 (93%) of D. elephantinus and 11 of 12 (92%) of D. venustus had 11 and nine arthropod species, respectively. Larval and nymphal stages of the tick Dermacentor occidentalis were the most prevalent parasite (77%) on D. elephantinus whereas the mesostigmatid mite Androlaelaps fahrenholzi was the most prevalent (56%) on D. venustus. The arthropod fauna of these two closely related rodents were similar with seven of the 14 arthropod species occurring on both host species. Two species of the host specific listrophorid mite of the genus Geomylichus were found on both hosts.

Median to radial nerve transfer to restore wrist and finger extension: technical nuances.

BACKGROUND: Traditional methods for restoring finger and wrist extension following radial nerve palsy include interposition nerve grafting or tendon transfers. We have described the utilization of distal nerve transfers for the restoration of radial nerve function in the forearm. OBJECTIVE: We review the neuroanatomy of the forearm and outline the steps required for the implementation of this transfer. METHODS AND RESULTS: We use a step-by-step procedural outline and detailed photographs, line drawings, and video to describe the procedure. CONCLUSION: This approach is technically feasible and is a reconstructive option for patients with this nerve deficit.

Matching of motor-sensory modality in the rodent femoral nerve model shows no enhanced effect on peripheral nerve regeneration.

The treatment of peripheral nerve injuries with nerve gaps largely consists of autologous nerve grafting utilizing sensory nerve donors. Underlying this clinical practice is the assumption that sensory autografts provide a suitable substrate for motoneuron regeneration, thereby facilitating motor endplate reinnervation and functional recovery. This study examined the role of nerve graft modality on axonal regeneration, comparing motor nerve regeneration through motor, sensory, and mixed nerve isografts in the Lewis rat. A total of 100 rats underwent grafting of the motor or sensory branch of the femoral nerve with histomorphometric analysis performed after 5, 6, or 7 weeks. Analysis demonstrated similar nerve regeneration in motor, sensory, and mixed nerve grafts at all three time points. These data indicate that matching of motor-sensory modality in the rat femoral nerve does not confer improved axonal regeneration through nerve isografts.

Retrograde labeling in peripheral nerve research: it is not all black and white.

Retrograde labeling has become an important method of evaluation for peripheral nerve regeneration after injury. We review the features of the commonly used retrograde tracers Fast Blue, Fluoro-Gold, and Fluoro Ruby in addition to the various application methods (conduit reservoir, intramuscular injection, and crystal powder application) and the techniques used to count stained neurons. Upon application of the staining techniques and dyes in a rat and mouse nerve injury model, Fluoro-Gold was found to stain the greatest number of neurons with all application methods. However, due to variability of staining intensity, neuron size, and background staining, it is difficult to count the stained neurons accurately. Fast Blue stains consistently using intramuscular injection in the mouse but fails to provide adequate staining using the muscle injection method in the rat model and shows high failure rates using the conduit reservoir technique. However, crystal dye application with Fast Blue to the cut nerve end provides excellent results. We believe that it is imperative to use the various tracers and application methods prior to their experimental use to develop a consistent standardized approach to retrograde labeling.

Neuroregenerative effects of preinjury FK-506 administration.

BACKGROUND: FK-506 is used in organ transplantation because it promotes neurite outgrowth in vitro and enhances neuroregeneration in peripheral nerve injury transection models. Immunosuppressive mechanisms of FK-506 are well defined, with demonstration of decreased neuroregenerative effects with delayed administration. The purpose of this study was to describe the effects of preinjury administration of FK-506 in rats with tibial nerve transection injury. METHODS: Eight inbred male Lewis rats per group in three separate groups underwent tibial nerve transection with primary repair. Group I received placebo, group II received FK-506 treatment at 1 day before surgery, and group III received FK-506 preloading 3 days before surgery. RESULTS: Histologic and histomorphometric results demonstrated the preload FK-506 group had superior results compared with the immediate FK-506 group. Both FK-506 groups were superior to the placebo group. The preload FK-506 demonstrated superior regeneration in mean total nerve fiber counts (p < 0.05), greater percentage neural tissue (p < 0.05), greater mean nerve fiber density (p < 0.05), and lower percentage of debris (p > 0.05). Mean nerve fiber widths were similar in the preload and immediate FK-506 groups but superior to the placebo group. CONCLUSION: These data suggest that enhancement of FK-506's neuroregenerative effect is enhanced when administered before nerve injury such as when performing elective surgery.

Effect of age on thrombosis and morbidity in the mouse-limb transplantation model.

Murine models of limb transplantation have been recently described. Because of the technical challenge, non-technical factors that influence the success rate and are easily controlled should be considered. This study investigated the effect of recipient animal age on anastomotic thrombosis, morbidity, and mortality. Twelve allogeneic heterotopic hindlimb transplants were performed using the femoral vessels with end-to-end arterial and end-to-side venous anastomoses. Group 1 (n=8) consisted of 2 to 3-month-old mice weighing 17 to 20 g, and Group 2 (n=7) included 7 to 8-month-old mice weighing 24 to 27 g. In Group 1, 6/8 (75 percent) transplants were successful, while in Group 2, only 1/7 (14 percent) allografts survived (p<0.05). A statistically significant difference in the incidence of vascular compromise of the ipsilateral recipient hindlimb was also noted (p<0.01). The authors conclude that although smaller, juvenile, inbred mice have a higher anastomotic patency rate, with greater collateral vasculature in the hindlimbs, and are therefore more suitable for limb transplantation research.

Anti-CD40 ligand monoclonal antibody induces a permissive state, but not tolerance, for murine peripheral nerve allografts.

Anti-CD40 ligand monoclonal antibody prevents the interaction between CD40 and its T-cell-based ligand, thereby resulting in selective inhibition of T cell costimulation without pan-T-cell suppression. This antibody has found application in several animal models of solid organ transplantation. This study investigated use of anti-CD40 ligand antibody to promote acceptance of nerve allografts. In Experiment 1, 40 BALB/cj mice with tibial nerve transplants were administered anti-CD40 ligand antibody, a control antibody, or no treatment. In Experiment 2, 40 BALB/cj mice underwent the same regimen as in Experiment 1, but were later challenged with a second nerve allograft 3 weeks after discontinuation of treatment. Animals treated with anti-CD40 ligand antibody in Experiment 1 exhibited improved functional recovery and greater mean fiber count, fiber density, and percent nerve fiber than animals treated with control antibody or no antibody (P < 0.05). These permissive effects on nerve regeneration were associated with immune unresponsiveness on Elispot assay. The benefit of anti-CD40 ligand therapy did not persist after withdrawal of treatment (Experiment 2). Active blockade of the CD40 costimulatory pathway with murine anti-CD40 ligand antibody therefore induces a permissive state conducive to nerve regeneration across allografts but does not establish long-term tolerance.

Use of anti-CD40 ligand monoclonal antibody as antirejection therapy in a murine peripheral nerve allograft model.

Monoclonal antibody directed against CD40 ligand prevents acute allograft rejection in several models of solid-organ transplantation. This study describes the use of CD40 ligand as antirejection therapy in a mouse peripheral nerve allograft model. C3H mice received 8-mm nerve isografts (n = 2) or nerve allografts from C57BL donors. Treated animals (n = 11) received anti-CD40 ligand antibody applied to the graft and by intraperitoneal injections postoperatively. At 3 weeks, nerve histology from treated animals was comparable to isografts, whereas untreated allografts demonstrated virtually no signs of regeneration. Walking-track analysis demonstrated a trend toward improved functional recovery in treated animals. In conclusion, blockade of the CD40 pathway suppresses nerve allograft rejection in mice, and facilitates regeneration comparable to isografts.