Improvement of Molecular Diagnosis Using Domain-Level Single-Nucleotide Variants by Eliminating Unexpected Secondary Structures.

Identification of single-nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain-level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double-stranded structure, specially designed probes are used to detect double-stranded properties and report abundant domain-level oligonucleotide information to improve the effective information in the detection results and complete domain-level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof-of-concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.

In-vivo T2-relaxation times of asymptomatic cervical intervertebral discs.

Limited research exists on T2-mapping techniques for cervical intervertebral discs and its potential clinical utility. The objective of this research was to investigate the in-vivo T2-relaxation times of cervical discs, including C2-C3 through C7-T1. Ten asymptomatic subjects were imaged using a 3.0 T MR scanner and a sagittal multi-slice multi-echo sequence. Using the mid-sagittal image, intervertebral discs were divided into five regions-of-interest (ROIs), centered along the mid-line of the disc. Average T2 relaxation time values were calculated for each ROI using a mono-exponential fit. Differences in T2 values between disc levels and across ROIs of the same disc were examined. For a given ROI, the results showed a trend of increasing relaxation times moving down the spinal column, particularly in the middle regions (ROIs 2, 3 and 4). The C6-C7 and C7-T1 discs had significantly greater T2 values compared to superior discs (discs between C2 and C6). The results also showed spatial homogeneity of T2 values in the C3-C4, C4-C5, and C5-C6 discs, while C2-C3, C6-C7, and C7-T1 showed significant differences between ROIs. The findings indicate there may be inherent differences in T2-relaxation time properties between different cervical discs. Clinical evaluations utilizing T2-mapping techniques in the cervical spine may need to be level-dependent.

Effects of arthroscopic anterior cruciate ligament reconstruction combined with sodium hyaluronate on knee function and inflammatory markers in anterior cruciate ligament injury patients with or without knee osteoarthritis.

BACKGROUND: Anterior cruciate ligament injury (ACLI) is a common sports injury of the knee joint, and ACLI patients often develop early knee osteoarthritis (KOA) after surgery. This may be due to the activation of a post-surgical inflammatory response. OBJECTIVES: To investigate the treatment efficacy of arthroscopic anterior cruciate ligament reconstruction (AACLR) combined with sodium hyaluronate (SH) in ACLI patients with and without KOA. MATERIAL AND METHODS: This prospective cohort study included 226 ACLI patients with or without KOA who were admitted between July 2015 and December 2018 into The Second Xiangya Hospital, Changsha, China. All patients received AACLR surgery combined with 50 mg SH. Serum levels of inflammatory markers were evaluated with enzyme-linked immunosorbent assay (ELISA), and knees were assessed using the Lysholm Knee Score and the International Knee Documentation Committee Knee Evaluation Form (IKDC). The range of motion of the knee joint was also measured. RESULTS: The mean disease course was 73.39 ±30.90 months for ACLI patients with KOA, which was significantly longer than for those without KOA (3.74 ±1.70 months). Also, surgery duration was remarkably longer for patients with KOA than it was for those without this disease. The Lysholm Knee Score and IKDC score, as well as the range of knee joint motion were significantly improved in all patients after treatment compared to baseline. However, no significant differences were found between the groups. One day, 3 days and 7 days after surgery, significantly higher inflammatory marker levels were found in the patients with KOA than in those without KOA. CONCLUSIONS: The AACLR combined with SH was efficacious as it improved knee function and inflammation in all patients, while patients without KOA exhibited a more rapid recovery from the post-surgical inflammatory response.

Chondroitin Polymerizing Factor (CHPF) promotes cell proliferation and tumor growth in human osteosarcoma by inhibiting SKP2's ubiquitination while activating the AKT pathway.

Osteosarcoma is a common malignant tumor occurring in children and young adults. Chondroitin sulfate (CS) participates in cell adhesion, cell division, and the formation of neural networks in the body, the biosynthesis of which requires the participation of glycosyltransferases. CHPF, a glycosyltransferase, plays a role in the extension of CS. Recently, CHPF's biological roles and functional importance in human diseases including malignant tumors have been widely discussed. However, whether CHPF is involved in osteosarcoma development and growth has not been revealed. The present work aimed to investigate the expression levels, functional significance and molecular mechanism of CHPF in osteosarcoma progression. Our results revealed that CHPF is strongly expressed in osteosarcoma tissues and cells. Furthermore, CHPF serves as a tumor promoter in the development and progression of osteosarcoma through enhancing cell proliferation and migration while suppressing apoptosis. Exploration of the mechanism by which CHPF promotes osteosarcoma indicated that CHPF promotes osteosarcoma through counteracting SKP2's ubiquitination and activating the Akt signaling pathway. For the first time, we clarified the roles of CHPF in osteosarcoma, and our results suggested that CHPF might be a novel therapeutic target in the treatment strategies for osteosarcoma.

Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling.

Enzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.

Entropy-driven catalytic amplification adjusted by stoichiometry for single-nucleotide variants detection with high abundance sensitivity.

Single-nucleotide variants (SNV) detection with high abundance sensitivity is of great significance in clinical application, molecular diagnostics and biological research. In this study, a high abundance sensitivity SNV detection strategy based on entropy-driven catalytic (EDC) amplification adjusted by stoichiometry is proposed. In EDC, the toehold exchange reaction is used to initiate subsequent catalytic reaction and can be adjusted by stoichiometry. When the by-product concentration in the toehold exchange reaction is excessive, the forward reaction will be inhibited, which can reduce or even block the unexpected reaction between the non-target and the probe. Meanwhile, some targets can still successfully take a toehold exchange reaction with the probe, thus completing the subsequent EDC. By adjusting the EDC, the SNV identification specificity of this system was improved and is superior to any single adjusted stoichiometry or EDC. When the low abundance target is detected from the mixture, this strategy enables SNV detection at 0.1% abundance with high abundance sensitivity. And even if the mixture contains three kind of 1000-fold interference sequences, this strategy can still discriminate the target SNV. Furthermore, the practical applicability of the adjusted EDC system was verified by p53 mutation discrimination in human urine.

DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants.

Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.

Erdheim-Chester disease with asymmetric talus involvement: A case report.

BACKGROUND: Erdheim-Chester disease (ECD) is a rare multi-system or multi-organ histiocytic proliferative disease with diverse clinical manifestations, and the development of the disease is complex, which makes clinical diagnosis and treatment difficult. The characteristic clinical manifestations include multi-organ involvement, especially in the symmetrical diaphysis and metaphysis of the bilateral extremities. ECD with a unilateral talus lesion is extremely rare. Here, we report an unusual case of ECD invading the asymmetric talus and tibia without involving other organs. The patient had good outcome after surgery. CASE SUMMARY: We report a case of a 67-year-old man who was referred to our outpatient department because of left ankle chronic pain for 5 years, which exacerbated after a foot sprain 6 mo previously. We discovered multiple sclerotic lesions of the tibia and talus on his previous X-ray films, which were initially missed in a local hospital. Therefore, enhanced computer computed tomography (CT) and magnetic resonance imaging were performed. These examinations showed multiple lesions in the bone marrow cavity of the left tibia, and cortical sclerosis and osteonecrosis of the left talus. Specimens were collected via bone puncture from the two lesions, and a final diagnosis of ECD was confirmed by pathological and immunohistochemical examinations. In addition, other auxiliary examinations including head CT, pulmonary CT, spinal CT, abdominal CT, cardiac ultrasound and thyroid ultrasound showed no obvious abnormalities. The patient underwent surgery for the tibia lesion scraping and talus lesion scraping combined with cement casting. The patient started on a progressive rehabilitation at 4 wk, and felt no pain after surgery. During a 2-year follow-up period, the patient exercised normally without pain, and there were no signs of recurrence. CONCLUSION: This study shows that surgery treatment may also achieve good results for ECD patients with only bone involvement.

Addressable activated cascade DNA sequential logic circuit model for processing identical input molecules.

Herein, we propose the state and activation mechanisms able to realize the unification of an input signal and addressable sequential execution. Furthermore, a DNA sequential logic circuit (SLC) model was designed and applied in constructing a DNA register that for the first time realizes the generalized storage of identical input molecules.

A DNA arithmetic logic unit for implementing data backtracking operations.

We present the application of redundant modules in the molecular cascade circuit, which can help trace the results of each logic gate. This provides a basis for finding the error position and judging the final circuit result to improve the circuit and the reliability of the system.

A domain-based DNA circuit for smart single-nucleotide variant identification.

According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.

In Vivo Characteristics of Nondegenerated Adjacent Segment Intervertebral Foramina in Patients With Degenerative Disc Disease During Flexion-Extension.

STUDY DESIGN: In vivo patient biomechanical study. OBJECTIVE: To investigate the dimensions of lumbar intervertebral foramen (LIVF) of patients with degenerative disc disease (DDD) during a flexion-extension motion of the body. SUMMARY OF BACKGROUND DATA: LIVF narrowing may result in nerve root compression. The area changes of degenerated and adjacent nondegenerated LIVFs in DDD patients under physiologic loading conditions are unknown. METHODS: Nine symptomatic low back pain patients with radiological evidence of L4-S1 DDD were recruited. Each subject was magnetic resonance imaging scanned for construction of three-dimensional lumbar vertebral models, and fluoroscopically imaged when the body extended from 45 flexion to full extension for reconstruction of LIVF dimensions. The data of the adjacent segment L3/4 and diseased segments L4/5 and L5/S1 were compared with a normal control group at 45 flexion, upright, and full extension of the body. RESULTS: The mean LIVF areas of DDD segments were significantly smaller than those of the normal subjects in all positions (P <0.05). In upright position, the LIVF areas of the DDD patients were 32.8% and 33.6% smaller than the normal subjects for L4/5 and L5/S1, respectively. For the adjacent L3/4, the LIVF area of the DDD patients was 32.3% smaller than that of the normal controls (P <0.05). The total change of L3/4 LIVF area in DDD patients from flexion to extension was significantly smaller than that of the normal subjects, but the changes in L4/5 and L5/S1 LIVF areas were similar between the two groups (P >0.05). CONCLUSION: Similar reductions of the LIVF dimensions were observed at the adjacent and the involved levels of the DDD patients, implying that biomechanical changes might have already occurred at the adjacent segment despite the lack of radiographic evidence of degeneration. Subsequent research should focus on the effects of surgical fusion on the biomechanical features of the adjacent segment. LEVEL OF EVIDENCE: N/A.

Sagittal plane rotation center of lower lumbar spine during a dynamic weight-lifting activity.

This study investigated the center of rotation (COR) of the intervertebral segments of the lower lumbar spine (L4-L5 and L5-S1 segments) in sagittal plane during a weight-lifting (3.6 kg in each hand) extension activity performed with the pelvis constrained. Seven healthy subjects were studied using a dual fluoroscopic imaging technique. Using the non-weightbearing, supine position during MRI scan as a reference, the average intervertebral flexion angles of the L4-L5 and L5-S1 were 6.6° and 5.3° at flexion position of the body, respectively, and were -1.8° and -3.5° at extension position of the body, respectively. The CORs of the lower lumbar spine were found segment-dependent and changed with the body postures. The CORs of the L4-L5 segment were at the location about 75% posterior from the anterior edge of the disc at flexion positions of the body, and moved to about 92% of the posterior portion of the disc at extension positions of the body. The CORs of the L5-S1 segment were at 95% posterior portion of the disc at flexion positions of the body, and moved outside of the posterior edge of the disc by about 12% of the disc length at extension positions of the body. These results could help understand the physiological motion characters of the lower lumbar spine. The data could also provide important insights for future improvement of artificial disc designs and surgical implantation of the discs that are aimed to reproduce normal spinal functions.

Anterior Lumbar Interbody Fusion for Degenerative Discogenic Low Back Pain: Evaluation of L4-S1 Fusion.

The treatment of degenerative discogenic pain is controversial, and anterior lumbar fusion for the treatment of degenerative discogenic low back pain has also been a controversial topic for over a generation.The aim of this systematic review was to evaluate the outcome of different anterior lumbar fusion levels for degenerative discogenic low back pain.In this study, we performed a clinical outcome subgroup analysis. The outcomes of 84 consecutive patients who underwent anterior lumbar interbody fusion from 2004 to 2009 were reviewed. The operative time, intraoperative blood loss, hospital stay, Oswestry Disability Index (ODI), visual analog scale (VAS) results, and complication rate were recorded separately.Medical indications were degenerative disc disease (73.8%), postdiscectomy disc disease (16.1%), and disc herniation (9.5%). Patients with severe spondylolysis or disc degeneration, with more than 3 or multilevel lesions, were excluded.The mean operative time was 124.5 ±â€Š10.9 min (range 51-248 min), the mean intraoperative blood loss was 242.1 ±â€Š27.7 mL (range 50-2700 mL), the mean hospital stay was 3.9 ±â€Š1.1 days (range 3-6 days), the mean preoperative VAS score was 7.5 ±â€Š1.4, and the mean preoperative ODI score was 60.0 ±â€Š5.7. At the 1-year follow-up, the mean postoperative VAS score was 3.3 ±â€Š1.3 and the mean postoperative ODI score was 13.6 ±â€Š3.4 (P < 0.05). L4-L5 disc fusion led to better clinical results than 2-level L4-L5/L5-S1 disc fusion. Additionally, the 2-level fusion of L4-L5/L5-S1 had better clinical results than the L5-S1 disc fusion at both the 1 and 2-year postoperative follow-ups regarding the VAS score and the ODI score. The rate of complications was more frequent in the 2-level L4-L5/L5-S1 group (27.3%) (group C) than in the L4-L5 group (9.1%) (group A) and the L5-S1 group (12.5%) (group B). There was no difference between the L4-L5 group (9.1%) and the L5-S1 group (12.5%). A venous tear occurred during surgery and was successfully repaired in 6 of the 84 patients. Also, out of the 84 patients, 6 were found with pseudarthrosis during the follow-up, and these patients underwent a spinal fusion with instrumentation, with a posterior approach after a mean of 1 year. The complications secondary to the surgical approach were persistent abdominal pain (1/84, 1.2%) and wound dehiscence (1/84, 1.2%).Anterior lumbar interbody fusion for L4-L5 had better clinical results than the 2-segmental L4-L5/L5-S1 disc fusion, and the 2-segmental L4-L5/L5-S1 disc fusion had better clinical results than the L5-S1 disc fusion. Also, the 2-segmental L4-L5/L5-S1 disc fusion had a higher complication rate (27.3%), but there was no difference between the L4-L5 group (9.1%) and the L5-S1 group (12.5%).

Atypical, multilevel and noncontiguous tuberculous spondylitis that affected the vertebrae of thoracic, lumbar and sacrum: a case report.

AIM: Tuberculous spondylitis (TS, also called Spinal tuberculosis, Pott's spine or Pott's disease) is a common extrapulmonary manifestation of tuberculosis (TB), but multilevel, noncontiguous TS cases are rare. METHODS: Physical examination, CT, MRI imaging, percutaneous biopsy and other lab tests were used to confirm the diagnosis. RESULT: we report a rare case of atypical, multilevel and noncontiguous TS in a 50-year-old woman. We found four noncontiguous osteolytic lesions in her spine that affected the Intervertebral joints of T10/11, L1/2, L3/4 and L5/S1. Patient was then treated conservatively with anti-TB drugs and was followed-up for about 1 year. The treatment turned out to be successful. CONCLUSION: The conservative anti-TB treatment was enough at least for this particular patient.

Surgical management for thoracic spinal tuberculosis posterior only versus anterior video-assisted thoracoscopic surgery.

STUDY DESIGN: A comparable retrospective study. OBJECT: To compare the clinical outcomes of surgical treatment by posterior only and anterior video-assisted thoracoscopic surgery for thoracic spinal tuberculosis (TSTB). METHOD: 145 patients with TSTB treated by two different surgical procedures in our institution from June 2001 to June 2014 were studied. All cases were retrospectively analyzed and divided into two groups according to the given treatments: 75 cases (32F/43M) in group A performed single-stage posterior debridement, transforaminal thoracic interbody fusion and instrumentation, and 70 cases (30F/40M) in group B underwent anterior video-assisted thoracoscopic surgery (VATS). Clinical and radiographic results in the two groups were analyzed and compared. RESULTS: Patients in group A and B were followed up for an average of 4.6±1.8, 4.4±1.2 years, respectively. There was no statistically significant difference between groups in terms of the operation time, blood loss, bony fusion, neurological recovery and the correction angle of kyphotic deformity (P>0.05). Fewer pulmonary complications were observed in group A. Good clinical outcomes were achieved in both groups. CONCLUSIONS: Both the anterior VATS and posterior approaches can effectively treat thoracic tuberculosis. Nevertheless, the posterior approach procedure obtained less morbidity and complications than the other.

In vivo dynamic changes of dimensions in the lumbar intervertebral foramen.

BACKGROUND CONTEXT: Previous studies have reported position-dependent changes of the lumbar intervertebral foramen (LIVF) dimensions at different static flexion-extension postures. However, the changes of the LIVF dimensions during dynamic body motion have not been reported. PURPOSE: The objective of this study was to investigate the in vivo dimensions of the LIVF during a dynamic weight-lifting activity. STUDY DESIGN/SETTING: This was a retrospective study. METHODS: Ten asymptomatic subjects were recruited for this study. Three-dimensional (3D) vertebral models of the lumbar segments from L2 to S1 were constructed for each subject using magnetic resonance images. The lumbar spine was then imaged using a dual fluoroscopic imaging system as the subject performed a dynamic weight-lifting activity from an upper body position of 45° to a maximal extension position. The in vivo positions of the vertebrae along the motion path were reproduced using the 3D vertebral models and the fluoroscopic images. The minimal area, height, and width of each LIVF during the dynamic body motion were analyzed. RESULTS: The LIVF area and width monotonically decreased with lumbar extension at all levels except L5-S1 (p<.05). On average, the LIVF area decreased by 7.4±6.7%, 10.8±7.7%, and 10.0±8.0% at the L2-L3, L3-L4, and L4-L5 levels, respectively, from the flexion to the upright standing position, and by 6.4±5.0%, 7.7±7.4%, and 5.1±5.1%, respectively, from the upright standing to the extension position. The LIVF height remained relatively constant at all segments during the dynamic activity. The foramen area, height, and width of the L5-S1 remained relatively constant throughout the activity. CONCLUSIONS: Human lumbar foramen dimensions show segment-dependent characteristics during the dynamic weight-lifting activity.

In vivo morphological features of human lumbar discs.

Recent biomechanics studies have revealed distinct kinematic behavior of different lumbar segments. The mechanisms behind these segment-specific biomechanical features are unknown. This study investigated the in vivo geometric characteristics of human lumbar intervertebral discs. Magnetic resonance images of the lumbar spine of 41 young Chinese individuals were acquired. Disc geometry in the sagittal plane was measured for each subject, including the dimensions of the discs, nucleus pulposus (NP), and annulus fibrosus (AF). Segmental lordosis was also measured using the Cobb method.In general, the disc length increased from upper to lower lumbar levels, except that the L4/5 and L5/S1 discs had similar lengths. The L4/5 NP had a height of 8.6±1.3 mm, which was significantly higher than all other levels (P<0.05). The L5/S1 NP had a length of 21.6±3.1 mm, which was significantly longer than all other levels (P<0.05). At L4/5, the NP occupied 64.0% of the disc length, which was significantly less than the NP of the L5/S1 segment (72.4%) (P<0.05). The anterior AF occupied 20.5% of the L4/5 disc length, which was significantly greater than that of the posterior AF (15.6%) (P<0.05). At the L5/S1 segment, the anterior and posterior AFs were similar in length (14.1% and 13.6% of the disc, respectively). The height to length (H/L) ratio of the L4/5 NP was 0.45±0.06, which was significantly greater than all other segments (P<0.05). There was no correlation between the NP H/L ratio and lordosis. Although the lengths of the lower lumbar discs were similar, the geometry of the AF and NP showed segment-dependent properties. These data may provide insight into the understanding of segment-specific biomechanics in the lower lumbar spine. The data could also provide baseline knowledge for the development of segment-specific surgical treatments of lumbar diseases.