Sex-split analysis of pathology and motor-behavioral outcomes in a mouse model of CLN8-Batten disease reveals an increased disease burden and trajectory in female Cln8mnd mice.

BACKGROUND: CLN8-Batten disease (CLN8 disease) is a rare neurodegenerative disorder characterized phenotypically by progressive deterioration of motor and cognitive abilities, visual symptoms, epileptic seizures, and premature death. Mutations in CLN8 results in characteristic Batten disease symptoms and brain-wide pathology including accumulation of lysosomal storage material, gliosis, and neurodegeneration. Recent investigations of other subforms of Batten disease (CLN1, CLN3, CLN6) have emphasized the influence of biological sex on disease and treatment outcomes; however, little is known about sex differences in the CLN8 subtype. To determine the impact of sex on CLN8 disease burden and progression, we utilized a Cln8mnd mouse model to measure the impact and progression of histopathological and behavioral outcomes between sexes. RESULTS: Several notable sex differences were observed in the presentation of brain pathology, including Cln8mnd female mice consistently presenting with greater GFAP+ astrocytosis and CD68+ microgliosis in the somatosensory cortex, ventral posteromedial/ventral posterolateral nuclei of the thalamus, striatum, and hippocampus when compared to Cln8mnd male mice. Furthermore, sex differences in motor-behavioral assessments revealed Cln8mnd female mice experience poorer motor performance and earlier death than their male counterparts. Cln8mnd mice treated with an AAV9-mediated gene therapy were also examined to assess sex differences on therapeutics outcomes, which revealed no appreciable differences between the sexes when responding to the therapy. CONCLUSIONS: Taken together, our results provide further evidence of biologic sex as a modifier of Batten disease progression and outcome, thus warranting consideration when conducting investigations and monitoring therapeutic impact.

Predicting transfer RNA gene activity from sequence and genome context.

Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined with difficulty in measuring transcript abundance and high sequence identity across transcripts, has severely limited our collective understanding of tRNA gene expression regulation and evolution. We establish sequence-based correlates to tRNA gene expression and develop a tRNA gene classification method that does not require, but benefits from, comparative genomic information and achieves accuracy comparable to molecular assays. We observe that guanine + cytosine (G + C) content and CpG density surrounding tRNA loci is exceptionally well correlated with tRNA gene activity, supporting a prominent regulatory role of the local genomic context in combination with internal sequence features. We use our tRNA gene activity predictions in conjunction with a comprehensive tRNA gene ortholog set spanning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other clades, as well as exploration of functional diversification of members of large gene families.

Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations.

High representation by ammonia-oxidizing archaea (AOA) in marine systems is consistent with their high affinity for ammonia, efficient carbon fixation, and copper (Cu)-centric respiratory system. However, little is known about their response to nutrient stress. We therefore used global transcriptional and proteomic analyses to characterize the response of a model AOA, Nitrosopumilus maritimus SCM1, to ammonia starvation, Cu limitation and Cu excess. Most predicted protein-coding genes were transcribed in exponentially growing cells, and of ~74% detected in the proteome, ~6% were modified by N-terminal acetylation. The general response to ammonia starvation and Cu stress was downregulation of genes for energy generation and biosynthesis. Cells rapidly depleted transcripts for the A and B subunits of ammonia monooxygenase (AMO) in response to ammonia starvation, yet retained relatively high levels of transcripts for the C subunit. Thus, similar to ammonia-oxidizing bacteria, selective retention of amoC transcripts during starvation appears important for subsequent recovery, and also suggests that AMO subunit transcript ratios could be used to assess the physiological status of marine populations. Unexpectedly, cobalamin biosynthesis was upregulated in response to both ammonia starvation and Cu stress, indicating the importance of this cofactor in retaining functional integrity during times of stress.

ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments.

High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, but RNAs containing modified nucleosides may escape detection when those modifications interfere with reverse transcription during RNA-seq library preparation. Here we describe AlkB-facilitated RNA methylation sequencing (ARM-seq), which uses pretreatment with Escherichia coli AlkB to demethylate N(1)-methyladenosine (m(1)A), N(3)-methylcytidine (m(3)C) and N(1)-methylguanosine (m(1)G), all commonly found in tRNAs. Comparative methylation analysis using ARM-seq provides the first detailed, transcriptome-scale map of these modifications and reveals an abundance of previously undetected, methylated small RNAs derived from tRNAs. ARM-seq demonstrates that tRNA fragments accurately recapitulate the m(1)A modification state for well-characterized yeast tRNAs and generates new predictions for a large number of human tRNAs, including tRNA precursors and mitochondrial tRNAs. Thus, ARM-seq provides broad utility for identifying previously overlooked methyl-modified RNAs, can efficiently monitor methylation state and may reveal new roles for tRNA fragments as biomarkers or signaling molecules.

The UCSC Archaeal Genome Browser: 2012 update.

The UCSC Archaeal Genome Browser (http://archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. By bringing together existing gene annotations, gene expression data, multiple-genome alignments, pre-computed sequence comparisons and other specialized analysis tracks, the genome browser is a powerful aggregator of varied genomic information. The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements. The browser currently contains 115 archaeal genomes, plus 31 genomes of viruses known to infect archaea. Some of the recently developed or enhanced tracks visualize data from published high-throughput RNA-sequencing studies, the NCBI Conserved Domain Database, sequences from pre-genome sequencing studies, predicted gene boundaries from three different protein gene prediction algorithms, tRNAscan-SE gene predictions with RNA secondary structures and CRISPR locus predictions. We have also developed a companion resource, the Archaeal COG Browser, to provide better search and display of arCOG gene function classifications, including their phylogenetic distribution among available archaeal genomes.

In-vitro kinematic testing of porcine cervical spine: a rotational manipulation model.

Although spinal manipulation is widely used in the management of neck and pain, its exact mechanisms and biomechancial effects are not clear. A porcine model was used to study the relative movements of intervertebral joints under spinal rotation maneuvers with different input angular displacements and thrust velocities. Ten porcine spines (C2/4) were fixed and mounted in a material testing machine. Rotational maneuvers with different input angular displacements (0.8, 1.5, 2 and 3 degrees) and thrust velocities (0.1 - 200 degrees/s) were applied to C2 with C4 fixed. Angular displacement induced at the adjacent level was measured and expressed as percentage of the applied angular displacement. For all the tested conditions, angular deformation at the adjacent level could not be avoided when an angular thrust was applied to the target level. The percentage of the angular displacement induced at the adjacent level was found to be dependent on both the input angular displacement and thrust velocity. If rapid thurst of manipulation is used to direct the input energy and motion at the target level with minimal interference at the adjacent levels, the applied angular displacement should not be too large and the thrust velocity should be within a medium velocity range.

Impaired dynamic balance control in adolescents with idiopathic scoliosis and abnormal somatosensory evoked potentials.

BACKGROUND: Both balance control dysfunction and dysfunction of the central nervous system have been proposed as being causative factors in adolescent idiopathic scoliosis (AIS), yet the relationship between these factors has not been investigated in detail. An intergroup comparative study was conducted to investigate the effect of abnormal somatosensory function on the dynamic balance parameters of girls with AIS. METHODS: The relationship between dynamic balance control and abnormal somatosensory function seen in AIS patients was examined by studying the dynamic balance parameters in normal controls, in AIS patients with normal posterior tibial nerve somatosensory cortical evoked potentials (PTN-SCEPs), and in AIS patients with abnormal PTN-SCEPs. Gait parameters were recorded in 18 AIS girls (8 showing abnormal PTN-SCEPs and 10 showing normal PTN-SCEPs). Eight healthy age-matched volunteers served as a control group. RESULTS: No significant left-right asymmetry of gait parameters was found for the controls or the AIS patients with normal PTN-SCEPs, whereas significantly higher gait parameters were found on the side of the curvature in the AIS patients with abnormal PTN-SCEPs. CONCLUSIONS: Somatosensory dysfunction in AIS patients shows to have an impact on dynamic balance control. Further studies to examine the association between somatosensory dysfunction and balance control and how they may be related to the etiology of AIS are recommended. LEVEL OF EVIDENCE: Diagnostic study, level IV (case-control study).

The effects of load carriage and bracing on the balance of schoolgirls with adolescent idiopathic scoliosis.

The balance function of children is known to be affected by carriage of a school backpack. Children with adolescent idiopathic scoliosis (AIS) tend to show poorer balance performance, and are typically treated by bracing, which further affects balance. The objective of this study is to examine the combined effects of school backpack carriage and bracing on girls with AIS. A force platform was used to record center of pressure (COP) motion in 20 schoolgirls undergoing thoraco-lumbar-sacral orthosis (TLSO brace) treatment for AIS. COP data were recorded with and without brace while carrying a backpack loaded at 0, 7.5, 10, 12.5 and 15% of the participant's bodyweight (BW). Ten participants stood on a solid base and ten stood on a foam base, while all participants kept their eyes closed throughout. Sway parameters were analyzed by repeated measures ANOVA. No effect of bracing was found for the participants standing on the solid base, but wearing the brace significantly increased the sway area, displacement and medio-lateral amplitude in the participants standing on the foam base. The medio-lateral sway amplitude of participants standing on the solid base significantly increased with backpack load, whereas significant increases in antero-posterior sway amplitude, sway path length, sway area per second and short term diffusion coefficient were found in participants standing on the foam base. The poorer balance performance exhibited by participants with AIS when visual and somatosensory input is challenged appears to be exacerbated by wearing a TLSO brace, but no interactive effect between bracing and backpack loading was found.

Reliability of radiographic intervertebral disc height measurement for in vivo rat-tail model.

Quantification of changes in intervertebral disc height is critical for studying intervertebral disc degeneration. Reliability of disc height measurement is therefore especially important for in vivo studies using animal models of disc degeneration. In this study, the effects of image intensity and percentage of disc width used for disc height measurement from radiographic images were evaluated in a rat-tail model. Radiographs were taken for 10 Sprague-Dawley rats using a standardized protocol. Average disc heights of the caudal 8-9 discs were determined using original and intensity adjusted images with different percentages of disc width. The average disc height was found to be significantly affected by both the image intensity and the percentage of disc width measured. A higher reliability was found in the measurement for image with adjusted intensity and using smaller disc width. Image intensity is suggested to be controlled and the disc width should be taken into account in quantifying the disc height.

The effect of prosthesis alignment on the symmetry of gait in subjects with unilateral transtibial amputation.

A high degree of gait symmetry is characteristic of healthy gait. The aim of this study is to examine the symmetry of various gait parameters in subjects with unilateral trans-tibial amputation over a range of acceptable anteroposterior translational and tilt alignments, and further to examine if a consistent alignment of highest symmetry can be found. Acceptable alignments were determined by bench, static and dynamic testing on level and non-level surfaces. A total of 15 kinetic and kinematic parameters were then measured in the seven subjects participating in this study. Results indicate that some parameters show consistently higher symmetries, particularly the vertical ground reaction force parameters and the stance duration, step length and time to full knee flexion during the swing phase. Symmetries in other parameters such as knee flexion at loading response, acceleration impulse, and peak anteroposterior propulsive force seem to have little relevance in determining whether the gait pattern for that prosthetic alignment is acceptable or not. While analysis of the symmetry of more relevant gait parameters may assist the prosthetist in consistently and objectively identifying a most symmetrical alignment within the acceptable range, further clinical study is required before any conclusions can be drawn regarding evaluation of symmetry as a tool in defining any optimum alignment.

The effect of load carriage on the gait of girls with adolescent idiopathic scoliosis and normal controls.

Adolescent idiopathic scoliosis (AIS) and load-bearing both appear to place similar demands on gait, but no data regarding the combined effects of load-bearing gait in subjects with AIS could be found. The gait patterns of 22 normal adolescent girls and 28 girls with mild AIS (Cobb angle<25 degrees ) were recorded at backpack loads of 0, 7.5, 10, 12.5 and 15% body weight. Temporal-distance and joint kinematic, moment and power parameters were analyzed by repeated measures ANOVA. Findings showed that backpack carriage places an increased demand on the musculature of the lower limb and results in a gait characterized by reduced pelvic motion and greater hip flexion-extension. AIS has a generally similar effect on gait kinematics as backpack carriage, with AIS subjects having significantly longer double support durations, shorter single support durations and lower knee joint power generation and absorption than normal subjects. No interaction between backpack load and AIS was found however, although investigation of parameters indicating a critical response to load showed that this typically occurred at lower backpack loads (7.5% body weight) in the AIS group. Overall, both AIS and load-bearing place increased demands on gait, but carriage of a loaded backpack does not appear to cause any greater demand on subjects with AIS than normal controls.

The effect of backpack weight on the standing posture and balance of schoolgirls with adolescent idiopathic scoliosis and normal controls.

Concerns have been raised regarding the effect of carrying a backpack on adolescent posture and balance, but the effect of backpack loading combined with other factors affecting balance, such as adolescent idiopathic scoliosis (AIS), has not been determined. This study examines the effects of backpack load on the posture and balance of schoolgirls with AIS and normal controls. The standing posture of 26 schoolgirls with mild AIS (mean age 13, Cobb angle 10-25 degrees ) and 20 age-matched normal schoolgirls were recorded without a backpack and while carrying a standard dual-strap backpack loaded at 7.5%, 10%, 12.5% and 15% of the subject's bodyweight (BW). Kinematics of the pelvis, trunk and head were recorded using a motion analysis system and centre of pressure (COP) data were recorded using a force platform. Reliable COP data could only be derived for 13 of the subjects with AIS. Increasing backpack load causes a significantly increased flexion of the trunk in relation to the pelvis and extension of the head in relation to the trunk, as well as increased antero-posterior range of COP motion. While backpack load appears to affect balance predominantly in the antero-posterior direction, differences between groups were more evident in the medio-lateral direction, with AIS subjects showing poor balance in this direction. Overall, carrying a backpack causes similar sagittal plane changes in posture and balance in both normal and AIS groups. Load size or subject group did not influence balance, but the additive effect of backpack carrying and AIS on postural control alters the risk of fall in this population. Therefore, load limit recommendations based on normal subjects should not be applicable to subjects with AIS.

Effects of backpack loading on the pulmonary capacities of normal schoolgirls and those with adolescent idiopathic scoliosis.

STUDY DESIGN: A prospective evaluation of the effects of backpack carriage on the pulmonary function of schoolgirls without spinal deformity versus those with adolescent idiopathic scoliosis (AIS). OBJECTIVE: To establish if recommended backpack load limits for normal schoolchildren are also appropriate for study participants with AIS. SUMMARY OF BACKGROUND DATA: The weight of schoolchildren's backpacks are of concern because of effects including compromise of pulmonary function. Impaired pulmonary function is also found with AIS, but the effect of backpack carriage on the respiratory parameters of schoolchildren with AIS has not previously been examined. METHODS: Forced vital capacity (FVC), forced expiratory volume (FEV1), peak expiratory flow (PEF), and forced expiratory flow (FEF25-75%) were recorded in 17 girls (mean age, 12 years) with moderate AIS (Cobb angle, 26 degrees-50 degrees) and 18 girls (mean age, 11 years) without musculoskeletal deformity during carriage of a backpack loaded at 0%, 5%, 7.5%, 10%, 12.5%, and 15% body weight in random order. Absolute values and proportions of reference values were analyzed by repeated-measures analysis of variance. RESULTS.: No interaction between load and group was found, indicating that backpack loading has a similar effect on the pulmonary function of both normal and AIS groups. However, all recorded pulmonary parameters were found to be significantly lower in the AIS than normal group, significantly so for the referenced FVC and PEF. A significant decrease in FVC and FEV1 was found with increasing backpack load, and the load at which these changes were found to be significant was lower than those established in previous studies. CONCLUSIONS: Pulmonary function may be more sensitive to backpack load than previously considered, especially when study participants with AIS are being considered, and the recommended loading limit of 10% body weight may not be applicable to schoolgirls with AIS.

Postural perturbation and muscular response following sudden release during symmetric squat and stoop lifting.

Squat and stoop lifting have been examined in some detail, but limited data exist regarding the sudden release of load during such lifting. Ten participants performed squat and stoop lifting trials with loads of 20, 40, 60 and 80N, and sudden release was randomly included in one of the lifting cycles. Postural perturbation was recorded via centre of pressure displacement using a force platform and the electromyographic response of trunk and lower limb muscles was recorded. Results indicated that irrespective of lifting posture, an 'ankle' response strategy to sudden release was elicited, where the anterior muscles of the lower limb contracted first, followed by the anterior trunk muscles, relaxation of the posterior trunk muscles and, finally, relaxation of the posterior lower limb muscles. The latency of muscles responding by contraction tended to decrease slightly with increasing load for both postures, while the latency of muscles responding by relaxation increased, resulting in increased trunk muscle co-contraction durations. The postural disturbance appeared to be greater for squat lifting than stoop lifting at the higher loads of 60 and 80N, as the centre of pressure moves significantly closer to the posterior limit of static stability (the line joining the heels).In terms of stability and muscular response, squat lifting may not be the most appropriate strategy if a sudden release of loads greater than approximately 50N is likely.

The effect of backpack load on the gait of normal adolescent girls.

Concerns regarding the effects of load carriage have led to recommendations that backpacks be limited to 10?-?15% of body weight, based on significant changes in physical performance. However, gait responses to backpack loads are not entirely consistent and there is a particular lack of data regarding load-bearing gait in adolescent females. Gait patterns of 22 normal adolescent girls were recorded at backpack loads of 0, 7.5, 10.0, 12.5 and 15.0% body weight. Temporal-distance, ground reaction force and joint kinematic, moment and power parameters were analysed by repeated measures ANOVA with factors of backpack load and side (left or right). Walking speed and cadence decreased significantly with increasing backpack load, while double support time increased. Kinematic changes were most marked at the proximal joints, with a decreased pelvic motion but a significant increase in the hip sagittal plane motion. Increased moments and power at the hip, knee and ankle showed increasing demand with backpack load. Parameters showed different responses to increasing load, and those that suggested a critical load indicated this to be approximately 10% body weight. While this may be due to a change in gait due to increased demand, further work is required to verify this and also to examine the cumulative effects of backpack load on the musculoskeletal system, which may be more appropriate in determining recommended load limits.

The kinematics and intra- and inter-therapist consistencies of lower cervical rotational manipulation.

The aim of this study was to determine the in vivo kinematics of cervical rotational manipulation in normal subjects and examine the consistency of this technique within and between therapists. A four camera motion analysis system operating at 120 Hz was used to measure the head on trunk angular displacements during manipulation performed by three therapists on eight subjects. One of the therapists performed the manipulation twice for each subject over separate sessions. A consistent pattern of de-rotation prior to thrust was found with little motion other than axial rotation during de-rotation and thrust. The pooled mean de-rotation displacement was 4.8 degrees and the pooled mean thrust angle was 11.3 degrees , but these varied widely, and none of the kinematic parameters recorded proved to be consistent within or between therapists. Most of the kinematic parameters were correlated with the exception of thrust duration. Qualitative analysis shows a consistent technique in cervical rotational manipulation. Pre-manipulation positioning of the head relative to the trunk was fairly consistent for a single therapist over separate sessions, but other than this, the kinematic parameters in cervical rotational manipulation are generally inconsistent within and between therapists.

Pure shear properties of lumbar spinal joints and the effect of tissue sectioning on load sharing.

STUDY DESIGN: An in vitro biomechanical study on lumbar intervertebral joints. OBJECTIVES: To examine the mechanical properties of lumbar motion segments under pure shear loading and establish whether a simple model for functional differentiation between the anterior column and the posterior elements is applicable. SUMMARY OF BACKGROUND DATA: Anteroposterior shear has been implicated as a major factor in spinal instability. There is a substantial amount of data on shear motion as a coupled part of flexion-extension; data on the pure shear properties of intervertebral joints is limited. METHODS: Eighteen human cadaver lumbar motion segments were subject to nondestructive testing under pure shear loads (anterior shear and posterior shear). An MTS standard testing machine was used to record the load-deformation characteristics of specimens subject to deformation at a constant rate to a maximum shear load of approximately 250 N. Tissue sectioning was then performed with the specimen mounted in the testing machine. Eight specimens were sectioned through the intervertebral disc, including the anterior and posterior longitudinal ligaments, and 8 specimens were sectioned through the pedicles to remove the posterior elements. The same deformation pattern applied to the intact specimen was then reapplied to the sectioned specimen, and the load-deformation characteristics following sectioning were evaluated. RESULTS: The shear stiffness of the intact segments were found to be higher in anterior shear (mean group A = 583.8, B = 607 N/mm) than in posterior shear (mean group A = 469, B = 438.4 N/mm). Section of the anterior column and adjacent longitudinal ligaments resulted in a mean stiffness decreased by 22.8% of the intact value under anterior shear and 23.9% under posterior shear. Much larger change in shear stiffness was seen, and the mean sectioned stiffness dropped by 77.7% in anterior shear and 79% in posterior shear after removal of the posterior elements. After the anterior column was sectioned, 12% and 18% increases in the deformation for anterior and posterior directions were seen, whereas a distinct increase in the deformations was found after posterior elements sectioned. CONCLUSIONS: The posterior elements of the lumbar spine are more efficient in resisting anterior and posterior shear loads. However, the anterior column will exhibit similar load-displacement characteristics if subject to greater deformations. The sum of the normalized mean shear loads of the anterior column and posterior elements sustained at maximum intact deformation is significantly different from the shear load sustained by the intact spine at the same deformation. A simple concept of load sharing between the anterior column and the posterior elements may not be valid.

Muscular and centre of pressure response to sudden release of load in symmetric and asymmetric stoop lifting tasks.

Sudden changes in load during asymmetric lifting may be associated with a particularly high risk of loss of balance and spinal injury. Centre of pressure (COP) motions and electromyographic responses of trunk and lower limb muscles were studied in 10 normal male volunteers during sudden release of 20, 40, 60 and 80N stoop lifting loads in symmetric and asymmetric postures. Similar overall COP responses and muscular response strategies to sudden release of load were seen in both postures, although the asymmetric posture showed a larger medio-lateral COP displacements and greater co-contraction asymmetries. While sudden release of load in asymmetric stoop lifting does not seem to involve a greater risk of fall than symmetric lifting, the muscular response results in more complex and asymmetric loading of the trunk, indicating greater localised segmental loading and therefore increased risk of tissue injury.

Changes in nuclear composition following cyclic compression of the intervertebral disc in an in vivo rat-tail model.

While in vitro studies have shown that mechanical loading can result in changes in the composition of intervertebral disc matrix, the effects of cyclic loading in vivo have not been considered. The objective of this study was to assess the effect of static and cyclic compression of different frequencies on the nuclear composition of the intervertebral disc. Thirty-six Sprague-Dawley rats were randomly divided into a control group (no pin insertion, no loading), a sham group (pins inserted in sixth and seventh caudal vertebrae, no loading), a static loading group (compression applied via pins) and cyclic loading groups (loading at 0.5, 1.5 or 2.5 Hz). Loading was applied for 1 h each day from the third to 17th day following pin insertion, and the caudal 5-6, 6-7 and 7-8 discs harvested to quantify proteoglycan content, collagen content and chondrocyte density in the nucleus pulposus. Static compression resulted in a significant reduction in total proteoglycan content as compared with the adjacent control disc, but this effect was not seen in any of the cyclic loading groups. However, comparison with the sham group appears to indicate an overall decrease in total proteoglycan content at the targeted and adjacent levels following cyclic loading. The 0.5 Hz loading group showed a significantly greater total proteoglycan content than all other compression groups, and also showed a lower total collagen content than the sham group. Results suggest that frequency dependent changes in composition occur in response to cyclic loading, but are not limited to the directly loaded disc alone. Further studies are required to verify this, but the choice of control appears to need careful consideration in all studies of this nature.