Effects of the major formaldehyde catalyzer ADH5 on phenotypes of fanconi anemia zebrafish model.

BACKGROUND: Fanconi anemia (FA) is a devastating hereditary disorder for which we desperately need a novel therapeutic strategy. It is caused by mutations in one of at least 22 genes in the FA pathway and is characterized by developmental abnormalities, bone marrow failure, and cancer predisposition. The FA pathway is required for the efficient repair of damaged DNA, including interstrand cross-links (ICL). Recent studies indicate formaldehyde as an ultimate endogenous cause of DNA damage in FA pathophysiology. Formaldehyde can form DNA adducts as well as ICLs by inducing covalent linkages between opposite strands of double-stranded DNA. METHODS AND RESULTS: In this study, we generated a disease model of FA in zebrafish by disrupting the ube2t or fancd2 gene, which resulted in a striking phenotype of female-to-male sex reversal. Since formaldehyde is detoxified from the body by alcohol dehydrogenase 5 (ADH5), we generated fancd2-/-/adh5-/- zebrafish. We observed a body size reduction and a lower number of mature spermatozoa than wild-type or single knockout zebrafish. To evaluate if increased activity in ADH5 can affect the FA phenotype, we overexpressed human ADH5 in fancd2-/- zebrafish. The progress of spermatogenesis seemed to be partially recovered due to ADH5 overexpression. CONCLUSIONS: Our results suggest potential utility of an ADH5 enzyme activator as a therapeutic measure for the clearance of formaldehyde and treatment of FA.

The relationship between characteristics of gait disturbance and injury patterns of the corticospinal tract and corticoreticular pathway in post-stroke patients: A case series of 3 patients.

RATIONALE: Corticospinal tract (CST) and corticoreticular pathway (CRP) injury patterns (i.e., the continuity of the nerve fibers) are associated with gait disturbance in post-stroke patients. In this case series study, we examined the case of 3 patients with different CST and CRP injury patterns and analyzed the characteristics of gait disturbance in each patient. PATIENT CONCERNS: Patient 1 (P1) was a 73-year-old woman who presented with paralysis of the right upper and lower extremities due to a left lacunar infarction. Patient 2 (P2) was a 41-year-old man who presented with paralysis of the right upper and lower extremities due to a left putamen hemorrhage. Patient 3 (P3) was a 57-year-old man who presented with paralysis of the left upper and lower extremities due to a right putamen hemorrhage. DIAGNOSIS: In P1, the CRP in the affected hemisphere was intact, but the CST was discontinuous. In P2, the CST in the affected hemisphere was intact, but the CRP was discontinuous. P3 was discontinuous in both CST and CRP in the affected hemisphere. OUTCOMES: Over time, all 3 patients improved to the level of gait independence, but they exhibited different gait patterns. Among them, P3 showed a markedly abnormal gait pattern that included spatiotemporal gait asymmetry, lateral shift of the trunk, and hip hiking. LESSONS: This case series study demonstrated that even if both the CST and CRP were injured, gait recovered to some extent (i.e., independent level-ground gait), but the abnormal gait pattern might remain remarkable.

REHABILITATION OUTCOMES IN PATIENTS WITH LOWER LIMB AMPUTATION RECEIVING HAEMODIALYSIS: A RETROSPECTIVE COHORT STUDY.

Objective: To compare the functional outcomes of patients with lower limb amputations receiving haemodialysis and those not receiving haemodialysis. Design: A retrospective cohort study. Patients: Patients with lower limb amputation who were admitted to a convalescent rehabilitation ward between January 2018 and December 2021. Methods: The primary outcome was the effectiveness of the Functional Independence Measure (FIM) during hospitalisation in the ward. Secondary outcomes included the total and subtotal (motor/cognitive) FIM scores at discharge, gain in the total and subtotal (motor/cognitive) FIM scores, K-level at discharge, length of hospital stay in the ward, rehabilitation time, and discharge destination. Outcomes were compared between the non-haemodialysis and haemodialysis groups. Results: A total of 28 patients (mean [standard deviation] age, 67.0 [11.9] years; men, 20) were enrolled in this study. Among them, 11 patients underwent haemodialysis. The FIM effectiveness was significantly higher in the non-haemodialysis group than in the haemodialysis group (median [interquartile range], 0.78 [0.72 - 0.81] vs 0.65 [0.28 - 0.75], p = 0.038). The amount of rehabilitation and all secondary outcomes were not significantly different between the groups (p > 0.05). Conclusion: Patients with lower limb amputation who were receiving haemodialysis had poorer FIM effectiveness than those not receiving haemodialysis.

Rehabilitation of a Patient with COVID-19 Who Underwent Right Transfemoral Amputation Due to Acute Limb Ischemia: A Case Report.

Background: Coronavirus disease 2019 (COVID-19) is associated with an increased risk of thrombotic complications. Nonetheless, there is a paucity of clinical knowledge regarding rehabilitation of patients with COVID-19 after lower-limb amputation. Case: A 74-year-old woman with COVID-19 was admitted to a university hospital. During hospitalization, she underwent right transfemoral amputation due to acute limb ischemia. Three months after admission, the patient was transferred to a convalescent rehabilitation ward in the same hospital. A femoral prosthesis was prescribed 2 weeks after her transfer to the rehabilitation ward. It featured ischial-ramal containment with a soft liner and belt suspension, 668-g multiple linkage-type safety knee joint (Imasen Engineering; M0781 SwanS), and a solid-ankle cushioned-heel foot. The total rehabilitation time during the patient's stay in the acute-care and rehabilitation wards was 65.5 h (0.99 h/day, 66 days) and 275.0 h (3.02 h/day, 91 days), respectively. In the rehabilitation ward, the patient underwent 54.4 h (19.8%) of muscle strength training, 48.1 h (17.5%) of comprehensive assessments, and 47.1 h (17.1%) of gait training. The patient was discharged home 6 months after admission, with a total Functional Independence Measure score of 120. The patient could walk slowly [44.2 s (0.23 m/s) in the 10 m-walk test] with a femoral prosthesis and a quad cane but exhibited limited endurance (75.0 m in the 6-min walk test). Discussion: Following appropriate rehabilitation, a patient was able to walk independently after lower-limb amputation despite the complication of COVID-19, although her walking ability was limited.

Transient receptor potential melastatin-7 in the rat dorsal root ganglion.

AIMS: Transient receptor potential melastatin-7 (TRPM7) is a selective cation permeable channel which plays important roles in cellular and developmental biology such as cell proliferation, survival, differentiation and migration. This channel is also known to be necessary for transmitter release in the peripheral nervous system. In this study, immunohistochemistry for TRPM7 was conducted in the rat lumbar dorsal root ganglion (DRG). METHODS: Triple immunofluorescence methods were used to demonstrate distribution of TRPM7 and its relationship to other TRP channels in the DRG. Retrograde tracing and double immunofluorescence methods were also performed to know peripheral targets of DRG neurons containing TRPM7 and TRP vanilloid 1 (TRPV1). In addition, transection of the sciatic nerve was conducted to demonstrate an effect of the nerve injury on TRPM7expression in the DRG. RESULTS: TRPM7-immunoreactivity was expressed by 53.9% of sensory neurons in the 4th lumbar DRG. TRPM7-immunoreactive (-IR) DRG neurons mostly had small (<600 µm²) and medium-sized (600-1200 µm²) cell bodies. By triple and double immunofluorescence methods, approximately 70% of TRPM7-IR DRG neurons contained TRPV1-immunoreactivity. Although the number of DRG neurons co-expressing TRPM7 and TRPM8 was small in the DRG, almost all of TRPM8-IR DRG neurons co-expressed TRPM7-immunoreactivity. By combination of retrograde tracing method and immunohistochemistry, TRPM7 was expressed by half of DRG neurons innervating the plantar skin (61.9%) and gastrocnemius muscle (51.2%), and 79.6% of DRG neurons innervating the periosteum. Co-expression of TRPM7 and TRPV1 among periosteum DRG neurons (75.7%) was more abundant than among cutaneous (53.2%) and muscular (40.4%) DRG neurons. DRG neurons which co-expressed these ion channels in the periosteum had smaller cell bodies compared to the skin and muscle. In addition, the sciatic nerve transection decreased the number of TRPM7-IR neurons in the DRG (approximately 60% reduction). The RT-qPCR analysis also demonstrated reduction of TRPM7 mRNA in the injured DRG. CONCLUSION: The present study suggests that TRPM7 is mainly located in small nociceptors in the DRG. The content of TRPM7 in DRG neurons is probably different among their peripheral targets. TRPM7 in DRG neurons may be able to respond to noxious stimulation from their peripheral tissues. The nerve injury can decrease the level of TRPM7 mRNA and protein in DRG neurons.

Influence of gait exercise using a walking-assist robot for swing-leg motion in hemiplegic stroke patients: a preliminary study focusing on the immediate effect.

Fujii R, Tamari M, Nonaka Y, Tamiya F, Hosokawa H, Tanaka S. Influence of gait exercise using a walking-assist robot for swing-leg motion in hemiplegic stroke patients: A preliminary study focusing on the immediate effect. Jpn J Compr Rehabil Sci 2022; 13: 49-55. Objective: We analyzed the effect of gait training using a walking-assist robot that assists a subject's knee joint movement and leg swing to achieve toe clearance of the paralyzed-side lower limb during treadmill walking. Methods: The subjects were 10 hemiplegic stroke patients in a rehabilitation ward. The intervention consisted of gait training using the Welwalk WW-1000 (Welwalk) robot for 40 min. Immediately before and after this intervention, a gait analysis of the patients' treadmill walking was performed by a three-dimensional motion capture system. Statistical analyses compared the foot-to-floor distance and the shortening of hip-toe length (SHTL) of the paralyzed side before and after the intervention, and examined the relationship between the change of lower-limb joint kinematics and toe clearance before and after the intervention. Results: The post-intervention SHTL was significantly lower compared to before the intervention, and there was a significant negative correlation between the change in the SHTL and the knee flexion angle from before to after the intervention. Conclusion: Gait exercise using the Welwalk could contribute to the acquisition of more normal leg-swing strategies.

Risk Factors and Prevalence of Deep Vein Thrombosis After the 2016 Kumamoto Earthquakes.

BACKGROUND: After previous earthquakes, a high prevalence of deep vein thrombosis (DVT) has been reported. We examined DVT prevalence and risk factors in evacuees of the Kumamoto earthquakes by performing mobile DVT screening at various evacuation centers around the epicenter. Methods and Results: For 1 month after the Kumamoto earthquake on 14 April 2016, mobile DVT screening using portable ultrasonography (US) was performed at 80 evacuation centers. Questionnaires, physical examination, and US of the lower limb were carried out, and simple D-dimer measurements were undertaken for DVT-positive examinees. The total number of examinees was 1,673, of whom 178 (10.6%) had DVT. The prevalence of DVT seemed to be gradually decreasing in the screening period, but age, use of sleep medication, prevalence of hypertension, dyslipidemia, leg edema, and lower leg varix were significantly higher in the DVT positive group than in the negative group. On multivariable logistic regression analysis, high age (≥70 years old), use of sleep medication, lower leg edema, and lower leg varix were significant predictors of DVT. In examinees with these 4 predictors, the DVT positive rate was 71.4%. CONCLUSIONS: In the first month after the Kumamoto earthquakes, DVT prevalence and severity, evaluated on D-dimer level, decreased with the passage of time. Mobile DVT screening indicated significant factors stratifying DVT risk in the evacuees.

Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.

As one of the few irreversible protein posttranslational modifications, proteolytic cleavage is involved in nearly all aspects of cellular activities, ranging from gene regulation to cell life-cycle regulation. Among the various protease-specific types of proteolytic cleavage, cleavages by casapses/granzyme B are considered as essential in the initiation and execution of programmed cell death and inflammation processes. Although a number of substrates for both types of proteolytic cleavage have been experimentally identified, the complete repertoire of caspases and granzyme B substrates remains to be fully characterized. To tackle this issue and complement experimental efforts for substrate identification, systematic bioinformatics studies of known cleavage sites provide important insights into caspase/granzyme B substrate specificity, and facilitate the discovery of novel substrates. In this article, we review and benchmark 12 state-of-the-art sequence-based bioinformatics approaches and tools for caspases/granzyme B cleavage prediction. We evaluate and compare these methods in terms of their input/output, algorithms used, prediction performance, validation methods and software availability and utility. In addition, we construct independent data sets consisting of caspases/granzyme B substrates from different species and accordingly assess the predictive power of these different predictors for the identification of cleavage sites. We find that the prediction results are highly variable among different predictors. Furthermore, we experimentally validate the predictions of a case study by performing caspase cleavage assay. We anticipate that this comprehensive review and survey analysis will provide an insightful resource for biologists and bioinformaticians who are interested in using and/or developing tools for caspase/granzyme B cleavage prediction.

In vivo targeted single-nucleotide editing in zebrafish.

To date, several genome editing technologies have been developed and are widely utilized in many fields of biology. Most of these technologies, if not all, use nucleases to create DNA double-strand breaks (DSBs), raising the potential risk of cell death and/or oncogenic transformation. The risks hinder their therapeutic applications in humans. Here, we show that in vivo targeted single-nucleotide editing in zebrafish, a vertebrate model organism, can be successfully accomplished with the Target-AID system, which involves deamination of a targeted cytidine to create a nucleotide substitution from cytosine to thymine after replication. Application of the system to two zebrafish genes, chordin (chd) and one-eyed pinhead (oep), successfully introduced premature stop codons (TAG or TAA) in the targeted genomic loci. The modifications were heritable and faithfully produced phenocopies of well-known homozygous mutants of each gene. These results demonstrate for the first time that the Target-AID system can create heritable nucleotide substitutions in vivo in a programmable manner, in vertebrates, namely zebrafish.

Deficiency of Serotonin in Raphe Neurons and Altered Behavioral Responses in Tryptophan Hydroxylase 2-Knockout Medaka (Oryzias latipes).

Serotonin (5-hydroxytryptamine [5-HT]) is a bioactive monoamine that acts as a neurotransmitter in the central and peripheral nervous system of animals. Teleost fish species have serotonergic neurons in the raphe nuclei of the brainstem; however, the role of 5-HT in the raphe neurons in teleost fish remains largely unknown. Here, we established a medaka (Oryzias latipes) strain with targeted disruption of tryptophan hydroxylase 2 (tph2) gene that is involved in the 5-HT synthesis in the raphe nuclei. Immunohistochemistry and mass spectrometry analysis revealed that the homozygous mutants (tph2Δ13/Δ13) lacked the ability to synthesize 5-HT in the raphe neurons. To investigate the effects of 5-HT deficiency in adult behaviors, the mutant fish were subjected to five behavioral paradigms (diving, open-field, light-dark transition, mirror-biting, and two-fish social interaction). The homozygous mutation caused a longer duration of freezing response in all examined paradigms and reduced the number of entries to the top area in the diving test. In addition, the mutants exhibited a decreased number of mirror-biting in the males and an increased contact time in direct social interaction between the females. These results indicate that this tph2-knockout medaka serves as a good model to analyze the effects of 5-HT deficiency in the raphe neurons.

Chordin and dickkopf-1b are essential for the formation of head structures through activation of the FGF signaling pathway in zebrafish.

The ability of the Spemann organizer to induce dorsal axis formation is dependent on downstream factors of the maternal Wnt/ß-catenin signaling pathway. The fibroblast growth factor (FGF) signaling pathway has been identified as one of the downstream components of the maternal Wnt/ß-catenin signaling pathway. The ability of the FGF signaling pathway to induce the formation of a dorsal axis with a complete head structure requires chordin (chd) expression; however, the molecular mechanisms involved in this developmental process, due to activation of FGF signaling, remain unclear. In this study, we showed that activation of the FGF signaling pathway induced the formation of complete head structures through the expression of chd and dickkopf-1b (dkk1b). Using the organizer-deficient maternal mutant, ichabod, we identified dkk1b as a novel downstream factor in the FGF signaling pathway. We also demonstrate that dkk1b expression is necessary, after activation of the FGF signaling pathway, to induce neuroectoderm patterning along the anteroposterior (AP) axis and for formation of complete head structures. Co-injection of chd and dkk1b mRNA resulted in the formation of a dorsal axis with a complete head structure in ichabod embryos, confirming the role of these factors in this developmental process. Unexpectedly, we found that chd induced dkk1b expression in ichabod embryos at the shield stage. However, chd failed to maintain dkk1b expression levels in cells of the shield and, subsequently, in the cells of the prechordal plate after mid-gastrula stage. In contrast, activation of the FGF signaling pathway maintained the dkk1b expression from the beginning of gastrulation to early somitogenesis. In conclusion, activation of the FGF signaling pathway induces the formation of a dorsal axis with a complete head structure through the expression of chd and subsequent maintenance of dkk1b expression levels.

Pharmacogenetic reactivation of the original engram evokes an extinguished fear memory.

Fear memory extinction has several characteristic behavioral features, such as spontaneous recovery, renewal, and reinstatement, suggesting that extinction training does not erase the original association between the conditioned stimulus (CS) and the unconditioned stimulus (US). However, it is unclear whether reactivation of the original physical record of memory (i.e., memory trace) is sufficient to produce conditioned fear response after extinction. Here, we performed pharmacogenetic neuronal activation using transgenic mice expressing hM3Dq DREADD (designer receptor exclusively activated by designer drug) under the control of the activity-dependent c-fos gene promoter. Neuronal ensembles activated during fear-conditioned learning were tagged with hM3Dq and subsequently reactivated after extinction training. The mice exhibited significant freezing, even when the fear memory was no longer triggered by external CS, indicating that the artificial reactivation of a specific neuronal ensemble was sufficient to evoke the extinguished fear response. This freezing was not observed in non-fear-conditioned mice expressing hM3dq in the same brain areas. These results directly demonstrated that at least part of the original fear memory trace remains after extinction, and such residual plasticity might reflect the persistent memory.

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data.

MOTIVATION: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. Efficient identification of targets for such regulatory RNAs needs not only discriminative power for positive and negative RNA-RNA interacting sequence data but also accurate prediction of interaction sites from positive data. Recently, a few studies have incorporated interaction site accessibility into their prediction methods, indicating the enhancement of predictive performance on limited positive data. RESULTS: Here we show the efficacy of our accessibility-based prediction model RactIPAce on newly compiled datasets. The first experiment in interaction site prediction shows that RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as compared with the state-of-the-art methods. In addition, the second experiment in discrimination between positive and negative interacting pairs reveals that the combination of accessibility-based methods including our approach can be effective to discern real interacting RNAs. Taking these into account, our prediction model can be effective to predict interaction sites after screening for real interacting RNAs, which will boost the functional analysis of regulatory RNAs. AVAILABILITY AND IMPLEMENTATION: The program RactIPAce along with data used in this work is available at https://github.com/satoken/ractip/releases/tag/v1.0.1 CONTACT: : ykato@rna.med.osaka-u.ac.jp or shingo@i.kyoto-u.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.

Chronic fluoxetine treatment induces anxiolytic responses and altered social behaviors in medaka, Oryzias latipes.

Medaka (Oryzias latipes) is a small freshwater teleost that is an emerging model system for neurobehavioral research and toxicological testing. The selective serotonin reuptake inhibitor class of antidepressants such as fluoxetine is one of the widely prescribed drugs, but little is known about the effects of these drugs on medaka behaviors. To assess the behavioral effects of fluoxetine, we chronically administrated fluoxetine to medaka adult fish and analyzed the anxiety-related and social behaviors using five behavioral paradigms (diving, open-field, light-dark transition, mirror-biting, and social interaction) with an automated behavioral testing system. Fish chronically treated with fluoxetine exhibited anxiolytic responses such as an overall increased time spent in the top area in the diving test and an increased time spent in center area in the open-field test. Analysis of socially evoked behavior showed that chronic fluoxetine administration decreased the number of mirror biting times in the mirror-biting test and increased latency to first contact in the social interaction test. Additionally, chronic fluoxetine administration reduced the horizontal locomotor activity in the open-field test but not the vertical activity in the diving test. These investigations are mostly consistent with previous reports in the other teleost species and rodent models. These results indicate that behavioral assessment in medaka adult fish will become useful for screening of effects of pharmaceutical and toxicological compounds in animal behaviors.

Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control.

Deciphering the association between life molecules and human diseases is currently an important task in systems biology. Research over the past decade has unveiled that the human genome is almost entirely transcribed, producing a vast number of non-protein-coding RNAs (ncRNAs) with potential regulatory functions. More recent findings suggest that many diseases may not be exclusively linked to mutations in protein-coding genes. The combination of these arguments poses the question of whether ncRNAs that play a critical role in network control are also enriched with disease-associated ncRNAs. To address this question, we mapped the available annotated information of more than 350 human disorders to the largest collection of human ncRNA-protein interactions, which define a bipartite network of almost 93,000 interactions. Using a novel algorithmic-based controllability framework applied to the constructed bipartite network, we found that ncRNAs engaged in critical network control are also statistically linked to human disorders (P-value of P = 9.8 × 10(-109)). Taken together, these findings suggest that the addition of those genes that encode optimized subsets of ncRNAs engaged in critical control within the pool of candidate genes could aid disease gene prioritization studies.

Distribution of transient receptor potential melastatin-8-containing nerve fibers in rat oral and craniofacial structures.

The transient receptor potential melastatin-8 (TRPM8) is a cold and menthol receptor located in the sensory ganglia. Immunohistochemistry for TRPM8 was performed on oral and craniofacial structures of the rat. TRPM8-immunoreactive (-IR) nerve fibers were detected in the oral mucous membrane. In the gingiva, TRPM8-IR nerve fibers were abundant beneath and within crestal and outer epithelia. Such nerve fibers were also common beneath and within taste buds in the incisive papilla. In addition, TRPM8-immunoreactivity was expressed by some taste bud cells in the papilla. Lips, periodontal ligaments and salivary glands as well as masticatory muscles and temporomandibular joints were mostly devoid of TRPM8-IR nerve fibers. A double immunofluorescence study indicated different distribution patterns of nerve fibers containing TRPM8 and calcitonin gene-related peptide in oral and craniofacial tissues. Retrograde tracing method also indicated that TRPM8-IR nerve fibers in the gingiva and incisive papilla originate from small sensory neurons in the trigeminal ganglion. TRPM8 may be associated with cool, cold nociceptive (

A Novel Method for Rearing Zebrafish by Using Freshwater Rotifers (Brachionus calyciflorus).

The zebrafish (Danio rerio) has become a powerful model organism for studying developmental processes and genetic diseases. However, there remain several problems in previous rearing methods. In this study, we demonstrate a novel method for rearing zebrafish larvae by using a new first food, freshwater rotifers (Brachionus calyciflorus). Feeding experiments indicated that freshwater rotifers are suitable as the first food for newly hatched larval fish. In addition, we revisited and improved a feeding schedule from 5 to 40 days postfertilization. Our feeding method using freshwater rotifers accelerated larval growth. At 49 dpf, one pair out of 10 pairs successfully produced six fertilized eggs. At 56, 63, and 71 dpf, 6 out of the 10 pairs constantly produced normal embryos. Our method will improve the husbandry of the zebrafish.

Intragastric administration of allyl isothiocyanate reduces hyperglycemia in intraperitoneal glucose tolerance test (IPGTT) by enhancing blood glucose consumption in mice.

We investigated the effects of allyl isothiocyanate (AITC) on the blood glucose levels of mice using an intraperitoneal glucose tolerance test. The intragastric administration of 25 mg/kg body weight AITC reduced the increase in blood glucose level after 2 g/kg body weight glucose was given intraperitoneally, compared with that of control mice. To elucidate the mechanism responsible for the reduction, respiratory gas analysis employing (13)C-labeled glucose was performed. The intragastrically administering AITC increased (13)CO2 emission, compared to vehicle, after intraperitoneal administration of (13)C-labeled glucose. This indicated that AITC increased the utilization of exogenously administered glucose, which was excessive glucose in the blood. To examine whether transient receptor potential (TRP) channels mediated this reduction in the blood glucose levels, we used TRPA1 and TRPV1 knockout (KO) mice. Intragastrically administering AITC reduced the increase in the blood glucose level in TRPA1 KO mice but not in TRPV1 KO mice. These findings suggest that dietary AITC might reduce the increases in blood glucose levels by increasing the utilization of excessive glucose in the blood by activating TRPV1.