Positive Emotional Responses to Socially Assistive Robots in People With Dementia: Pilot Study

Background

Interventions and care that can evoke positive emotions and reduce apathy or agitation are important for people with dementia. In recent years, socially assistive robots used for better dementia care have been found to be feasible. However, the immediate responses of people with dementia when they are given multiple sensory modalities from socially assistive robots have not yet been sufficiently elucidated.

Objective

This study aimed to quantitatively examine the immediate emotional responses of people with dementia to stimuli presented by socially assistive robots using facial expression analysis in order to determine whether they elicited positive emotions.

Methods

This pilot study adopted a single-arm interventional design. Socially assistive robots were presented to nursing home residents in a three-step procedure: (1) the robot was placed in front of participants (visual stimulus), (2) the robot was manipulated to produce sound (visual and auditory stimuli), and (3) participants held the robot in their hands (visual, auditory, and tactile stimuli). Expression intensity values for "happy," "sad," "angry," "surprised," "scared," and "disgusted" were calculated continuously using facial expression analysis with FaceReader. Additionally, self-reported feelings were assessed using a 5-point Likert scale. In addition to the comparison between the subjective and objective emotional assessments, expression intensity values were compared across the aforementioned 3 stimuli patterns within each session. Finally, the expression intensity value for "happy" was compared between the different types of robots.

Results

A total of 29 participants (mean age 88.7, SD 6.2 years; n=27 female; Japanese version of Mini-Mental State Examination mean score 18.2, SD 5.1) were recruited. The expression intensity value for "happy" was the largest in both the subjective and objective assessments and increased significantly when all sensory modalities (visual, auditory, and tactile) were presented (median expression intensity 0.21, IQR 0.09-0.35) compared to the other 2 patterns (visual alone: median expression intensity 0.10, IQR 0.03-0.22; P<.001; visual and auditory: median expression intensity 0.10, IQR 0.04-0.23; P<.001). The comparison of different types of robots revealed a significant increase when all stimuli were presented by doll-type and animal-type robots, but not humanoid-type robots.

Conclusions

By quantifying the emotional responses of people with dementia, this study highlighted that socially assistive robots may be more effective in eliciting positive emotions when multiple sensory stimuli, including tactile stimuli, are involved. More studies, including randomized controlled trials, are required to further explore the effectiveness of using socially assistive robots in dementia care.

Neuropsychological tests used for dementia assessment in Japan: Current status

AIM

This study aimed to investigate the assessment tools dementia specialists use in clinical practice, reasons for their use and assessment-related factors.

METHODS

A questionnaire survey was carried out from 15 September 2021 to 20 October 2021 among 1858 dementia specialists in Japan, with responses obtained via mail or using a Web form accessed via a Web address.

RESULTS

Of the 1858 specialists who were sent the questionnaire, 574 responded, yielding a response rate of 32.2%. Almost all respondents stated that the main purposes of neuropsychological testing were to identify the pathophysiology and aid diagnosis. Most respondents identified behavioral and psychological symptoms of dementia as important factors for assessment. The most commonly used tests were the Hasegawa Dementia Scale-Revised and Mini-Mental State Examination, often used as screening tools. The Mini-Mental State Examination, Clock Drawing Test and Cube Copying Test were common assessments carried out directly by specialists. Quality of life and burden of care were less commonly assessed.

CONCLUSIONS

Despite the main purpose of carrying out neuropsychological tests on dementia patients is to "understand the pathophysiology" and "aid in diagnosis," many assessment methods were chosen as screening methods carried out in a short time during clinic hours. The lack of evaluation of care burden and QOL, considered important by specialists, is an issue for the future in treating people with dementia, a life disability. Geriatr Gerontol Int 2024; 24: 102-109.

Comparison of usefulness between the Mini-Balance Evaluation Systems Test and the Berg Balance Scale for measuring balance in patients with subacute stroke: a prospective cohort study

Introduction

The aim of this study was to compare the clinical applicability of the Mini-Balance Evaluation Systems Test and the Berg Balance Scale for measuring balance in inpatients with subacute stroke.

Methods

This was a prospective observational study which included 58 consecutive patients admitted to a convalescent rehabilitation hospital with a first-ever stroke and who met the inclusion/exclusion criteria. The Mini-Balance Evaluation Systems Test and the Berg Balance Scale were used to assess patient balance at admission and discharge. The ceiling and floor effects and responsiveness of each balance score were examined. In addition, receiver operating characteristic analysis based on each balance score at admission was used to examine its discriminative power to predict ambulatory independence and falls during hospitalization.

Results

The mean (standard deviation) change between admission and discharge for each balance scale was 4.4 (4.7) for the Mini-Balance Evaluation Systems Test and 8.3 (10.0) for the Berg Balance Scale, with standard response means, a measure of responsiveness of 0.9 (large) and 0.8 (medium), respectively. Each balance score at admission almost equally predicted gait independence and fallers during hospitalization. On the contrary, only the distribution of scores on the Berg Balance Scale at discharge showed a ceiling effect, with 25 patients (43%) obtaining a perfect score.

Discussion

The Mini-Balance Evaluation Systems Test may be useful as a balance measure for inpatients with subacute stroke because it is less susceptible to ceiling effects and more responsive than the Berg Balance Scale.

Direction-dependent differences in the quality and quantity of horizontal reaching in people after stroke

Arm reaching is often impaired in individuals with stroke. Nonetheless, how aiming directions influence reaching performance and how such differences change with motor recovery over time remain unclear. Here, we elucidated kinematic parameters of reaching toward various directions in people with poststroke hemiparesis in the subacute phase. A total of 13 and 15 participants with mild and moderate-to-severe hemiparesis, respectively, performed horizontal reaching in eight directions with their more-affected and less-affected sides using an exoskeleton robotic device at the time of admission to and discharge from the rehabilitation ward of the hospital. The movement time, path length, and number of velocity peaks were computed for the mild group (participants able to reach toward all eight directions). In addition, the total amount of displacement (i.e., movement quantity) toward two simplified directions (mediolateral or anteroposterior) was evaluated for the moderate-to-severe group (participants who showed difficulty in completing the reaching task). Motor recovery was evaluated using the Fugl-Meyer assessment. The mild group showed worse values of movement parameters during reaching in the anteroposterior direction, irrespective of the side of the arm or motor recovery achieved. The moderate-to-severe group exhibited less movement toward the anteroposterior direction than toward the mediolateral direction at admission; however, this direction-dependent bias in movement quantity decreased, with the movement expanding toward the anteroposterior direction with motor recovery at discharge. These results suggest that direction-dependent differences in the quality and quantity of reaching performance exist in people after stroke, regardless of the presence or severity of hemiparesis. This highlights the need to consider the task work area when designing rehabilitative training.NEW & NOTEWORTHY Arm reaching, a fundamental function required for the upper extremities, is often impaired after stroke due to muscle weakness and abnormal synergies. Nonetheless, how aiming directions influence performance remains unclear. Here, we report that direction-dependent differences in the quality and quantity of reaching performance exist, surprisingly regardless of the presence or severity of hemiparesis. This result highlights the need to consider the task work area when designing rehabilitative training.

Feasibility and efficacy of an activity-monitoring approach using pedometer in patients undergoing subacute rehabilitation: A pilot study

Wearable devices for the quantification of walking have recently been adopted for gait rehabilitation. To apply this method in subacute rehabilitation settings, this approach must be effective in these populations and implemented as a feasible method in terms of adherence and safety, especially the risk of falling. This study aimed to investigate the feasibility and efficacy of an activity monitoring approach in subacute rehabilitation using a commercially available pedometer validated with slow walking. This randomized controlled study with blinded assessors recruited 29 patients admitted to a rehabilitation ward. The participants were randomly assigned to either the feedback (intervention) or the no-feedback (control) group. Participants in both groups received at least 120 min of therapy sessions every day for 6 or 7 days per week while wearing pedometers on their unaffected ankles from the day they were permitted to walk independently till discharge. Only participants in the feedback group received weekly encouragement and the next goals. The primary outcome was the change in the 6-minute walking distance (Δ6MD). Feasibility (percentage of pedometer data acquisition days in the total observational period and the number of falls) and other efficacy outcomes (step counts, gait speed, 30-seconds chair stand test, Berg Balance Scale, and Timed Up and Go Test) were also evaluated. Regarding feasibility outcomes, the data acquisition rate was 94.1% and the number of falls during the observation period was one in the feedback group. Regarding efficacy outcomes, Δ6MD was not significantly greater in the feedback group [mean (standard deviation): 79.1 (51.7) m] than in the no-feedback group [86.1 (65.4) m] (p = 0.774) and the other five secondary outcomes showed no between-group difference. Considering the large number of steps per day in both groups [6,912 (4,751) and 5,600 (5,108) steps in the feedback and no-feedback group, respectively], the effect of the intended intervention might have been masked by the effect of simply wearing pedometers in the control group. This study revealed that the activity monitoring approach using an ankle-worn pedometer was practical in terms of adherence and safety. Further clinical trials are required to elucidate ways to effectively use wearable devices in subacute rehabilitation.

Effectiveness of Self-Monitoring Approach Using Fitness Trackers to Improve Walking Ability in Rehabilitation Settings: A Systematic Review

Background: A self-monitoring approach utilizing fitness trackers that provide feedback regarding physical activities has been recently applied to rehabilitation patients to promote voluntary walking activities. Although this approach has been proven to increase physical activity, it is uncertain whether the intervention improves walking ability.

Aim: This review investigated whether the additional self-monitoring approach using activity trackers would improve walking ability in any type of rehabilitation setting.

Methods: A systematic search was performed in four databases [PubMed (MEDLINE), The Cochrane Library, SPORTDiscus, and Cumulative Index to Nursing and Allied Health Literature] to identify studies that examined the self-monitoring approach combined with rehabilitative intervention vs. the same rehabilitative intervention only in participants with any unhealthy conditions. Two review authors independently assessed the eligibility of all the retrieved English literature published from 2009 to 2019, then discussed the final inclusion. The risk of bias was assessed referring to the criteria of the Cochrane Risk of Bias tool. The key findings were synthesized using narrative synthesis. In addition, a quantitative synthesis was conducted when more than two studies investigating the same disease were identified.

Results: Eleven randomized controlled trials satisfied the eligibility criteria, nine of which had a lower risk of bias. The types of diseases included stroke, chronic obstructive pulmonary disease (COPD), cancer, Parkinson's disease, hemophilia, peripheral artery disease, post-total knee arthroplasty, and geriatric rehabilitation. Eight studies reported measures of walking endurance and four reported measures of gait speed. In the quantitative synthesis of two studies investigating COPD, there was a significant between-group difference in terms of changes in the 6-min walking distance from the baseline, which was favorable to the additional self-monitoring intervention group (mean difference: 13.1 m; 95% confidence interval, 1.8–24.5; 2 studies, 124 participants; p = 0.02; I² = 0%). Other available data revealed no consistent evidence regarding effectiveness of the intervention.

Conclusions: The findings indicate that there is little evidence suggesting the effectiveness of the self-monitoring approach in improving walking ability in rehabilitation settings. However, a weak recommendation for patients with stable COPD was implicated in the quantitative synthesis. Further research would be required to explore the best indications for this self-monitoring approach.

Systematic Review Registration: CRD 42020157695.

Outcomes of Dysphagia Following Stroke: Factors Influencing Oral Intake at 6 Months After Onset

PURPOSE

This study aimed to describe recovery of dysphagia after stroke. We determined the proportion of stroke survivors with dysphagia on admission, discharge, and 6 months after stroke. Additionally, the factors affecting oral feeding 6 months after stroke were explored.

METHODS

A total of 427 acute stroke patients were recruited prospectively. Presence of dysphagia was evaluated on admission, weekly until recovery was achieved, and at discharge. We compared stroke survivors with dysphagia who had complete recovery, who had dysphagia but achieved oral feeding, and who required tube feeding. Patient-reported eating ability was evaluated at 6 months. Patients who achieved oral feeding by 6 months were compared to those who had persistent tube feeding need.

RESULTS

Fifty-five percent of stroke survivors had dysphagia on initial evaluation (3.1 ± 1.4 days after admission) and 37% at discharge (21.1 ± 12.4 days). At 6 months, 5% of patients required tube feeding. Among those who had dysphagia at initial evaluation, 32% had resolution of dysphagia within two weeks, 44% had dysphagia but started oral feeding before discharge, and 23% required alternative means of alimentation (nasogastric tube feeding, percutaneous endoscopic gastrostomy, parental nutrition) throughout hospitalization. At 6 months, 90% of stroke survivors who achieved oral feeding by discharge continued with oral feeding. Patients who achieved oral feeding after discharge had less cognitive impairments on admission and a higher speech therapist intervention rate after discharge.

CONCLUSIONS

More than half of stroke survivors had dysphagia but the vast majority were able to return to oral feeding by 6 months. Cognitive function and dysphagia rehabilitation interventions were associated with return to oral feeding after hospital discharge.

Reliability of the thumb localizing test and its validity against quantitative measures with a robotic device in patients with hemiparetic stroke

Objectives

To examine the inter-rater reliability of the thumb localizing test (TLT) and its validity against quantitative measures of proprioception.

Methods

The TLT was assessed by two raters in a standardized manner in 40 individuals with hemiparetic stroke. Inter-rater reliability was examined with weighted Kappa. For the quantitative measures, a bimanual matching task in a planar robotic device was performed. Without vision, each participant moved the unaffected hand to the perceived mirrored location of the affected hand, which was passively moved by the robot. Three measures were taken after 54 trials: Variability, trial-to-trial variability of the mirrored-matched locations; Area, the ratio of the area enclosed by the active hand relative to the passive hand; and Shift, systematic shifts between the passive and active hands. The correlation between the TLT and each robotic measure was examined with Spearman’s rank correlation coefficient.

Results

The overall weighted kappa of the TLT was 0.84 (P<0.001). The TLT correlated highly with Area (r = -0.71, P<0.001) and moderately with Variability (r = 0.40, P = 0.011). No significant correlation was found between the TLT and Shift.

Conclusions

The TLT had a high inter-rater reliability, and was validated against quantitative measures of proprioception reflecting the perceived area of movement and variability of the limb location.

Reliability and Validity of the Japanese Version of the Mini-balance Evaluation Systems Test in Patients with Subacute Stroke

Objective

The objective of the current study was to evaluate the reliability and validity of the Japanese version of the Mini-Balance Evaluation Systems Test (J-Mini-BESTest) in patients with subacute stroke.

Methods

Eighteen patients who had suffered a first hemiplegic stroke (mean age, 59.1 ± 27.0 years) and had been admitted to convalescent rehabilitation wards were enrolled. The J-Mini-BESTest, the Berg Balance Scale (BBS), and the functional reach test (FRT) were used to assess balance. Four physical therapists (PTs) observed and scored the J-Mini-BESTest while another PT conducted the test. The interrater reliability of the J-Mini-BESTest was assessed using intraclass correlation coefficients (ICC[2,1]) for the total and section scores, and kappa statistics for each item. Internal consistency of the five raters was assessed using Cronbach's alpha. Concurrent validity of the J-Mini-BESTest was assessed against the BBS and FRT using Spearman's correlation coefficients.

Results

The ICC[2,1] of the total and section scores were 0.90 (95% confidence interval: 0.81-0.95) and 0.63-0.85, respectively. Cronbach's alphas were 0.80-0.87. The kappa statistics were 0.47-1.00. The scores of the J-Mini-BESTest were significantly correlated with those of the BBS (rho=0.66, p=0.006) but not with those of the FRT (rho=-0.36, p=0.189).

Conclusion

The J-Mini-BESTest showed excellent inter-rater reliability and internal consistency. Although the J-Mini-BESTest was not correlated with the FRT, it was significantly correlated with the BBS. The J-Mini-BESTest is a reliable and valid tool for evaluating dynamic balance in patients with subacute stroke.

Clinical usefulness and validity of robotic measures of reaching movement in hemiparetic stroke patients

BACKGROUND

Various robotic technologies have been developed recently for objective and quantitative assessment of movement. Among them, robotic measures derived from a reaching task in the KINARM Exoskeleton device are characterized by their potential to reveal underlying motor control in reaching movements. The aim of this study was to examine the clinical usefulness and validity of these robot-derived measures in hemiparetic stroke patients.

METHODS

Fifty-six participants with a hemiparetic arm due to chronic stroke were enrolled. The robotic assessment was performed using the Visually Guided Reaching (VGR) task in the KINARM Exoskeleton, which allows free arm movements in the horizontal plane. Twelve parameters were derived based on motor control theory. The following clinical assessments were also administered: the proximal upper limb section in the Fugl-Meyer Assessment (FMA-UE(A)), the proximal upper limb part in the Stroke Impairment Assessment Set (SIAS-KM), the Modified Ashworth Scale for the affected elbow flexor muscles (MAS elbow), and seven proximal upper limb tasks in the Wolf Motor Function Test (WMFT). To explore which robotic measures represent deficits of motor control in the affected arm, the VGR parameters in the paretic arm were compared with those in the non-paretic arm using the Wilcoxon signed rank test. Then, to explore which VGR parameters were related to overall motor control regardless of the paresis, correlations between the paretic and non-paretic arms were examined. Finally, to investigate the relationships between the robotic measures and the clinical scales, correlations between the VGR parameters and clinical scales were investigated. Spearman's rank correlation coefficients were used for all correlational analyses.

RESULTS

Eleven VGR parameters on the paretic side were significantly different from those on the non-paretic side with large effect sizes (|effect size| = 0.76-0.87). Ten VGR parameters correlated significantly with FMA-UE(A) (|r| = 0.32-0.60). Eight VGR parameters also showed significant correlations with SIAS-KM (|r| = 0.42-0.49), MAS elbow (|r| = 0.44-0.48), and the Functional Ability Scale of the WMFT (|r| = 0.52-0.64).

CONCLUSIONS

The robot-derived measures could successfully differentiate between the paretic arm and the non-paretic arm and were valid in comparison to the well-established clinical scales.

Development of a new scale for dysphagia in patients with progressive neuromuscular diseases: the Neuromuscular Disease Swallowing Status Scale (NdSSS)

Dysphagia is one of the most critical problems in patients with progressive neuromuscular diseases. However, clinically useful and practical scales to evaluate dysphagia are limited. Therefore, the aim of this study was to develop such a scale. An 8-stage Neuromuscular Disease Swallowing Status Scale (NdSSS) was developed and tested for its inter- and intrarater reliabilities, concurrent validity, and responsiveness. The NdSSS was used to evaluate 134 patients with Duchenne muscular dystrophy (DMD) and 84 patients with amyotrophic lateral sclerosis (ALS). Inter- and intrarater reliabilities were examined with weighted kappa statistics. Concurrent validity was assessed by correlating the NdSSS with the existing scales [Functional Oral Intake Scale (FOIS), Functional Intake LEVEL Scales (FILS), and ALS Functional Rating Scale-Revised Swallow (ALSFRS-R Sw)], using Spearman's correlation coefficients. Responsiveness was determined with the standardized response mean (SRM). For inter- and intrarater reliabilities, the weighted kappas were 0.95 and 1.00, respectively, for DMD; and 0.98 and 0.98, respectively, for ALS. The NdSSS showed strong correlations with the FOIS (rs = 0.87 for DMD, rs = 0.93 for ALS, p < 0.001), FILS (rs = 0.89 for DMD, rs = 0.92 for ALS, p < 0.001), and ALSFRS-R SW (rs = 0.93, p < 0.001). SRMs were 0.65 for DMD and 1.21 for ALS. The SRM was higher in DMD patients for the NdSSS than for the other scales, while it was similar in ALS patients and the other scales. Our originally developed NdSSS demonstrated sufficient reliability, validity, and responsiveness in patients with DMD and ALS. It is also useful in evaluating dysphagia in patients with progressive neuromuscular diseases.

The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like proteins

We previously reported the sequence of YL8A, one of the two genes encoding yeast ribosomal protein YL8. With the aim of conducting an evolutionary study we have cloned and sequenced a second gene, YL8B. The disruption of both genes is lethal. Unlike other duplicated ribosomal protein genes, each open reading frame is interrupted by two introns containing long conserved sequences. A comparison of nucleotide and amino-acid sequences reveals that the duplication of the YL8 gene must have occurred very recently. Alignment and phylogenetic analysis of the amino-acid sequences of YL8-related proteins from various species show the existence not only of YL8 ribosomal proteins but also of a family of YL8-like proteins. These are present in at least three species of yeast and seem to be functionally distinct from ribosomal proteins.

Yeast ribosomal proteins: XIV. Complete nucleotide sequences of the two genes encoding Saccharomyces cerevisiae YL16

We isolated and sequenced YL16A and YL16B encoding ribosomal protein YL16 of Saccharomyces cerevisiae. The two nucleotide sequences within coding regions retain 91.1% identity, and their predicted sequences of 176 amino acids show 93.8% identity. Out of the ribosomal protein sequences from various organisms currently available, no counterpart to YL16 could be found.

Yeast ribosomal proteins: XIII. Saccharomyces cerevisiae YL8A gene, interrupted with two introns, encodes a homolog of mammalian L7

We isolated and sequenced a gene, YL8A, encoding ribosomal protein YL8 of Saccharomyces cerevisiae. It is one of the two duplicated genes encoding YL8 and is located on chromosome VII while the other is on chromosome XVI. The haploid strains carrying disrupted YL8A grew more slowly than the parent strain. The open reading frame is interrupted with two introns. The predicted amino acid sequence reveals that yeast YL8 is a homolog of mammalian ribosomal protein L7, E.coli L30 and others.

Yeast ribosomal proteins: XII. YS11 of Saccharomyces cerevisiae is a homologue to E. coli S4 according to the gene analysis

We isolated and sequenced a gene, YS11A, encoding ribosomal protein YS11 of Saccharomyces cerevisiae. YS11A is one of two functional copies of the YS11 gene, located on chromosome XVI and transcribed in a lower amount than the other copy which is located on chromosome II. The disruption of YS11A has no effect on the growth of yeast. The 5'-flanking region contains a similar sequence to consensus UASrpg and the T-rich region. The open reading frame is interrupted with an intron located near the 5'-end. The predicted amino acid sequence reveals that yeast YS11 is a homologue to E. coli S4, one of the ram proteins, three chloroplast S4s and others out of the ribosomal protein sequences currently available.

Sequence and functional similarity between a yeast ribosomal protein and the Escherichia coli S5 ram protein

The accurate and efficient translation of proteins is of fundamental importance to both bacteria and higher organisms. Most of our knowledge about the control of translational fidelity comes from studies of Escherichia coli. In particular, ram (ribosomal ambiguity) mutations in structural genes of E. coli ribosomal proteins S4 and S5 have been shown to increase translational error frequencies. We describe the first sequence of a ribosomal protein gene that affects translational ambiguity in a eucaryote. We show that the yeast omnipotent suppressor SUP44 encodes the yeast ribosomal protein S4. The gene exists as a single copy without an intron. The SUP44 protein is 26% identical (54% similar) to the well-characterized E. coli S5 ram protein. SUP44 is also 59% identical (78% similar) to mouse protein LLrep3, whose function was previously unknown (D.L. Heller, K.M. Gianda, and L. Leinwand, Mol. Cell. Biol. 8:2797-2803, 1988). The SUP44 suppressor mutation occurs near a region of the protein that corresponds to the known positions of alterations in E. coli S5 ram mutations. This is the first ribosomal protein whose function and sequence have been shown to be conserved between procaryotes and eucaryotes.

Yeast ribosomal proteins: XI. Molecular analysis of two genes encoding YL41, an extremely small and basic ribosomal protein, from Saccharomyces cerevisiae

Two genes encoding ribosomal protein YL41 were cloned from Saccharomyces cerevisiae chromosomal DNA. Both genes contain an uninterrupted region of only 75 nucleotides coding for a protein of 3.3 kD. Within the coding regions the nucleotide sequences are virtually identical, whereas in both the 5'- and 3'-flanking regions the two genes differ significantly from each other. The deduced protein shows an arginine and lysine content of 68 percent, i.e., 17 out of 25 residues, and the basic residues are evenly distributed over the molecule. When compared to the ribosomal protein sequences currently available no counterpart to YL41 could be found in prokaryotes and it seems likely that YL41 is a eukaryote-specific ribosomal protein.

Examination of protein sequence homologies. VII. The complementary molecular coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and L10

Recently reported P1, P2 and metabacteria line sequences of transposition-type 'A' proteins, equivalent to Escherichia coli ribosomal protein L7/L12, were examined using a correlation method which evaluates the sequence similarity quantitatively. As the sequences could be aligned along the alignment previously constructed for 25 various 'A' proteins, the inclusive alignment further supports the previous claims concerning the rule of "preservation units" and the transpositional regeneration for metabacterial and eukaryotic 'A' proteins. Yeasts contain multispecies of P1 and P2 line genes and their P1 line sequences show low correlation coefficient values compared to other P1 line sequences, indicating a great evolutionary distance between lower and higher eukaryotes. Five sequences of protein P0 from metabacteria, yeast, and human, of which about 20 residues at the C termini are homologous with those of their own transposition-type 'A' proteins, were similarly examined. The N-terminal three-quarters of the sequences align naturally and the first two-thirds of the alignment could involve the E. coli L10 (EL10) sequence. An alignment of the remaining sequences at the C termini was established, relying on the well-matching sequence similarities between the metabacteria 'A' protein and their P0 protein sequences. Finally, the C-terminal halves of P0 protein sequences corresponded with almost overall sequences of the transposition-type 'A' proteins. The gene fusion of a protein might have resulted in the formation of the P0 proteins. A coupling of this gene fusion and the transposition of prototype 'A' proteins may have given rise to the complementary molecular transformations required for the development toward higher organism cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Examination of protein sequence homologies: V. New perspectives on evolution between bacterial and chloroplast-type ferredoxins inferred from sequence evidence

Sequence homologies among 34 chloroplast-type ferredoxins were examined using a computer program that quantitatively evaluates the extent of sequence similarity as a correlation coefficient. The resultant alignment contains six gaps representing insertions or deletions of some residues, all of which are located such that they precisely preserve the domains of structural fragments as determined by crystallographic data on Spirulina platensis ferredoxin. In the search for any total correlation between the chloroplast-type and 27 bacterial ferredoxins, 1891 comparison matrices prepared for possible combinations indicated that the bacterial basal sequence of 55 residues has been conserved evolutionarily in the chloroplast-type sequences corresponding to residue positions 36-90 of Spirulina platensis ferredoxin. In addition, the bacterial "connector sequence" region was found to be conserved. These findings strongly suggest that the bacterial and chloroplast-type ferredoxins descended from a common ancestor, and branched off after the bacterial gene duplication, whereas the chloroplast-type ferredoxins originally were generated by duplicating the already duplicated bacterial gene, i.e., by "double-duplication."

Examination of protein sequence homologies. VI. The evolution of Escherichia coli L7/L12 equivalent ribosomal proteins ('A' proteins), and the tertiary structure

Sequence homologies among 23 complete and two partial sequences of ribosomal 'A' proteins from eukaryotes, metabacteria, eubacteria and chloroplasts, equivalent to Escherichia coli L7/L12, were examined using a correlation method that evaluates sequence similarity quantitatively. Examination of 325 comparison matrices prepared for possible combinations of the sequences indicates that 'A' protein sequences can be classified into two types: one is the "prototype" from eubacteria and chloroplasts, and the other is the "transposition type" from eukaryotes and metabacteria, which must have resulted from the internal transposition of the prototype sequence. The transposition type of eukaryotes can further be classified into P1 and P2 lines. Sequences of the P1 line are closer to those of metabacteria than to those of the P2 line. Eleven gaps, as deletion or insertion sites of amino acid residues, are necessary for an alignment of all the sequences. According to the crystallographic data for the C-terminal fragment (CTF) from E. coli L7, all the gaps involved in the CTF are located between segments that correspond to structural and functional elements such as alpha helix, beta strand, turning loop or hinge part. The existence of specific "preservation units" in these molecules is suggested. In contrast, the transposition site is located at the center of an alpha helix element that is involved in a folding domain, indicating that the transposition event was extremely drastic.

Structural comparison of 26S rRNA-binding ribosomal protein L25 from two different yeast strains and the equivalent proteins from three eubacteria and two chloroplasts

The sequences of Saccharomyces carlsbergensis ribosomal protein (r-protein) SL25* and its equivalents from Candida utilis (CL25), Escherichia coli (EL23), Bacillus stearothermophilus (BL23), Mycoplasma capricolum (ML23), Marchantia polymorpha chloroplasts (McpL23), and Nicotiana tabacum chloroplasts (NcpL23) were examined using a computer program that evaluates the extent of sequence similarity by calculating correlation coefficients for each pair of residues in two proteins from a number of physical properties of individual amino acids. Comparison matrices demonstrate that the prokaryotic sequences (including McpL23 and NcpL23) can be aligned unambiguously by introducing small internal deletions/insertions at three specific positions. A similar comparison brought to light a clear evolutionary relationship between the prokaryotic and the yeast proteins despite the fact that visual inspection of these sequences revealed only limited similarity. The alignment deduced from this comparison shows the two yeast r-proteins to have acquired a long (50-60 amino acids) N-terminal extension as well as a 13-amino acid-long deletion near the C-terminus. The significance of these findings in terms of the evolution of r-proteins in general and the biological function of various parts of the SL25 protein in particular is discussed.

Examination of protein sequence homologies: IV. Twenty-seven bacterial ferredoxins

Sequence homologies of 27 bacterial ferredoxins were examined using a computer program that quantitatively evaluates extent of similarity as a correlation coefficient. The results of a similarity search among the sequences demonstrated that the basal sequence consists of a pair of extremely similar segments of 26 amino acids connected by a three-amino acid group. The segment pairs, which would have arisen from gene duplication, are termed the first and second units. Because of the gene duplication, the connector sequence appears to have been introduced as a structurally important chain reversal. Each of the two units contains four cysteine residues, which are inserted one by one among seven, two, two, three, and eight amino acid alignments, respectively. The bacterial ferredoxins were categorized with regard to basal constitution as follows: group 1, in which both units closely conform to the basal structure; group 2, in which the second unit is modified in a characteristic manner among members; group 3, in which the first unit is modified in a characteristic manner, while the conforming second unit is accompanied by a long accessory sequence; group 4, in which there are modifications before and/or after the units, of which the respective central domains remain nearly intact; and group 5, where only the former of two Fe:S cluster ligation sets of four cysteines is estimated to remain intact, whereas the latter set is extremely modified. It is noteworthy that throughout all bacterial ferredoxins, one of two cysteine sets never fails to be completely intact and, moreover, the connector of three amino acids also exists intact. Based on this grouping and on the correspondences among the groups, average correlation coefficients among all members were computed, and the respective evolutionary relationships were examined. The results supported the proposition that transposition had occurred in the Azotobacter-type ferredoxins of group 3.

Examination of protein sequence homologies: III. Ribosomal protein YS25 from Saccharomyces cerevisiae and its counterparts from Schizosaccharomyces pombe, rat liver, and Escherichia coli

The sequences of the ribosomal proteins YS25, SP-S28, RL-S21, and Ec-S6, from Saccharomyces cerevisiae, Schizosaccharomyces pombe, rat liver, and Escherichia coli, respectively, have been examined using a computer program that searches for homologous tertiary structures. Matrices of comparisons among the eukaryotic sequences show that they match each other sequentially without any internal gaps. The average values of the correlation coefficients obtained from the comparison matrices are higher for the first halves of the sequences than for the latter halves. This result suggests that the first halves of the sequences may represent a more important domain than the latter halves. The comparison matrices between the eukaryotic and bacterial sequences of ribosomal proteins, however, do not show sequentially arranged homology, though there are six well-matching segments arranged in different orders in the two types of sequences. This implies that the eukaryotic sequences of the ribosomal protein were reconstituted by two internal transpositions and six deletions of 4-12 residues each from the ancestral sequence during the divergence between bacterial and eukaryotic genes. These findings may give insight into structural and quantitative studies of evolutionary divergence between eukaryotes and prokaryotes.

In vivo phosphorylation of Saccharomyces cerevisiae ribosomal protein S10 by cyclic-AMP-dependent protein kinase

Using wild-type Saccharomyces cerevisiae strains and mutants which are defective in the regulatory subunit of cyclic-AMP-dependent protein kinase (bcy1) and phosphoprotein phosphatase activity (ppd1), we demonstrated that a cyclic-AMP-dependent protein kinase phosphorylated the S. cerevisiae ribosomal protein S10 in vivo. S10 was not dephosphorylated in bcy1 or ppd1 mutants after heat shock. The phosphorylated forms of S10 were diminished during the stationary phase in bcy1 and ppd1 mutants as well as in wild-type cells.

Primary structures of ribosomal protein YS25 from Saccharomyces cerevisiae and its counterparts from Schizosaccharomyces pombe and rat liver

Protein YS25 and its counterparts, SP-S28 and rat S21 [nomenclature according to Sherton, C. C., & Wool, I. G. (1972) J. Biol. Chem. 247, 4460-4467], from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and rat liver cytoplasmic ribosomes, respectively, were sequenced by a combination of various enzymatic digestions and/or chemical cleavage. Proteins YS25 and SP-S28 consist of 87 amino acid residues, and rat S21 consists of 83. The amino termini are all N alpha-acetylated. The amino-terminal halves of the protein molecules are highly conserved (73-85% homologies) in contrast to the carboxy-terminal parts. Overall, rat S21 is 54% homologous to YS25 and 57% to SP-S28, despite a 76% homology between YS25 and SP-S28. Direct comparison with the available prokaryotic ribosomal protein sequences did not reveal any significant homology.

Examination of protein sequence homologies: I. Eleven Escherichia coli L7/L12-type ribosomal "A" protein sequences from eubacteria and chloroplast

Seven complete and four partial sequences of Escherichia coli L7/L12-type ribosomal "A" proteins obtained from various bacteria (E. coli, Bacillus subtilis, Micrococcus lysodeikticus, Rhodopseudomonas spheroides, Desulfovibrio vulgaris, Streptomyces griseus, Bacillus stearothermophilus, Clostridium pasteurianum, Arthrobacter glacialis, and Vibrio costicola) and spinach chloroplast have been reexamined using a computer program that searches for homologous tertiary structures. Comparison matrices for the sequences show that they match the sequence of E. coli L7 (EL7) if one assumes the insertion or deletion of certain residues at sites corresponding to residues 1, 38, 49, and 92 of EL7. That two additional insertion points are found only in the spinach chloroplast protein suggests that the chloroplast protein probably diverged from the bacterial forms. Further phylogenetic relationships among these 11 prokaryote-type "A" proteins are discussed with respect to average correlation coefficients computed, taking into account the existence of the gaps.

Immunological evidence for structural homology between Drosophila melanogaster (S14), rabbit liver (S12), Saccharomyces cerevisiae (S25), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomal proteins

Specific antibodies directed against Drosophila melanogaster acidic ribosomal protein S14 were used in a comparative study of eucaryotic and procaryotic ribosomes by immunoblotting and enzyme-linked immunosorbent assays. Common antigenic determinants and, thus, structural homology were found between D. melanogaster, Saccharomyces cerevisiae (S25), rabbit liver (S12), Bacillus subtilis (S6), and Escherichia coli (S6) ribosomes.

Yeast ribosomal proteins: VII. Cytoplasmic ribosomal proteins from Schizosaccharomyces pombe

The cytoplasmic ribosomal proteins from a fission yeast Schizosaccharomyces pombe were analysed by two-dimensional polyacrylamide gel electrophoresis. Seventy-three protein species were identified in the 80S ribosome, and named SP-S1 to SP-S33 and SP-L1 to SP-L40 in the small and large subunits, respectively. Many of these proteins could be correlated to those of Saccharomyces cerevisiae on the basis of their electrophoretic mobilities. Eleven proteins were isolated from the 80S ribosome, and their amino acid compositions were determined. Of these, SP-S6, SP-L1, SP-L12, SP-L15, SP-L17, SP-L27, SP-L36 and SP-L40c and d were sequenced from their amino-termini. SP-S28 and SP-L2 appear to have their amino-termini blocked. These results were compared with the data available for the S. cerevisiae and rat liver ribosomal proteins. The S. cerevisiae counterparts of the eight proteins mentioned above were found to be YS4, YL1, YL10, YL14, YL35, YL40 and YL44c and d, respectively. The rat liver counterparts of SP-S6, SP-L1, SP-L27 and SP-L40c and d were the rat S6, L4, L37 and P2, respectively. Comparison of the partial sequences of these ribosomal proteins suggests that these two yeasts are relatively far apart, phylogenetically.

Isolation of seventeen proteins and amino-terminal amino acid sequences of eight proteins from cytoplasmic ribosomes of yeast

Seventeen ribosomal proteins of Saccharomyces cerevisiae were isolated from small ribosomal subunits and disodium ethylenediaminetetraacetate treated 80S ribosomes by chromatography on a column of carboxymethylcellulose and/or by filtration through Sephacryl S-200. The isolated proteins are YS4, YS7, YS8, YS9, YS10, YS12, YS14, YS18, YS23, YS29, YL11, YL13, YL16, YL17, YL22, YL38, and YL40 [nomenclature according to Otaka & Osawa (1981) [Otaka, E., & Osawa, S. (1981) Mol. Gen. Genet. 181, 176-182]]. The purification procedures and the amino acid compositions of these proteins are presented. Amino-terminal amino acid sequences of YS4, YS6, YS11, YS15, YS16, YS22, YL10, and YL31 have been determined and compared with those from rat liver [Wittmann-Liebold, B., Geissler, A. W., Lin, A., & Wool, I. G. (1979) J. Supramol. Struct. 12, 425-433] and Halobacterium cutirubrum [Matheson, A. T., Möller, W., Amons, R., & Yaguchi, M. (1980) in Ribosomes: Structure, Function and Genetics (Chambliss, G., et al., Eds.) pp 297-332, University Park Press, Baltimore, MD; M. Yaguchi, unpublished experiments].

Purification and characterization of 30S ribosomal proteins from Bacillus subtilis: correlation to Escherichia coli 30S proteins

Twenty proteins were isolated from the 30S ribosomal subunits of Bacillus subtilis and their amino acid compositions and amino-terminal amino acid sequences were determined. These results were compared with the data of Escherichia coli 30S ribosomal proteins and the structural correspondence of individual ribosomal proteins has been established between B. subtilis and E. coli. Post-translational modifications of amino-terminal amino acids of the ribosomal proteins which have been found in E. coli are almost absent in B. subtilis with the exception of acetylated forms of S9.

Isolation and characterization of twenty-three ribosomal proteins from large subunits of yeast

The proteins of large ribosomal subunits from Saccharomyces cerevisiae were separated into 25 fractions by chromatography on columns of carboxymethylcellulose (CMC). Twenty-three proteins were then purified from the 12 CMC fractions by filtration through Sephadex G-75, Sephadex G-100, and Sephacryl S-200, and/or by phosphocellulose column chromatography. The isolated proteins are YP 1, YP 2, YP 9, YP 11, YP 13', YP 16, YP 18, YP 26, YP 39, YP 41, YP 42, YP 42', YP 44, YP 45, YP 47', YP 52a, YP 53, YP 55, YP 59, YP 62, YP 68, YP A1, and YP A2. The molecular weight and amino acid composition of these proteins are presented.

Isolation and characterization of fourteen ribosomal proteins from small subunits of yeast

A method for preparation of a large amount of ribosomal subunits from Saccharomyces cerevisiae by a Ti-15 zonal rotor is described. The proteins of the small subunits (ca. 50 000 A260 units) were separated into 22 fractions by chromatography on carboxymethylcellulose columns. Fourteen proteins were then purified from the ten chromatographic fractions by filtration through Sephadex G-100 or Sephacryl S--200. The isolated proteins are YP 6, YP 7, YP 9, YP 12, YP 14', YP 14'', YP 28, YP 38, YP 45, YP 50, YP 52, YP 58, YP 63, and YP 70. The molecular weight and amino acid compositions of these proteins are presented.

Yeast ribosomal proteins. I. Characterization of cytoplasmic ribosomal proteins by two-dimensional gel electrophoresis

The cytoplasmic 80s ribosomal proteins from the cells of yeast Sachharomyces cerevisiae were analysed by SDS two-dimensional polyacrylamide gel electrophoresis. Seventyfour proteins were identified and consecutively numbered from 1 to 74. Upon oxidation of the 80s proteins with performic acid, ten proteins (no. 15, 20, 35, 40, 44, 46, 49, 51, 54 and 55) were dislocated on the gel without change of the total number of protein spots. Five proteins (no. 8, 14, 16, 36 and 74) were phosphorylated in vivo as seen in 32P-labelling experiments. The large and small subunits separated in low magnesium medium were analyzed by the above gel electrophoresis. At least forty-five and twenty-eight proteins were assumed to be in the large and small subunits, respectively. All proteins found in the 80s ribosomes, except for no. 3, were detected in either subunit without appearance of new spots. The acidic protein no. 3 seems to be lost during subunit dissociation.

Correlation of 30S ribosomal proteins of Escherichia coli fractionated on carboxymethyl-cellulose column chromatography to the standard nomenclature

The nomenclature proposed by Otaka et al. (1968) for the 30S ribosomal protein components of Escherichia coli as separated by carboxymethyl(CM)-cellulose column chromatography was adopted in several papers in which the genetic loci for many 30S ribosomal proteins on the E. coli chromosome were determined. In order to compare these data with those obtained in other laboratories, the 30S ribosomal proteins fractionated by CM-cellulose chromatography were correlated with thestandard nomenclature proposed by Wittmann et al. (1971).

Differentiation of the ribosomal protein compositions in the genus Escherichia and its related bacteria

Compositions of the ribosomal proteins of 60 bacterial strains belonging to the genus Escherichia and its related genera were examined by use of a column of carboxymethyl cellulose. The ribosomes were classified into seven groups and were further differentiated into several types (subgroups) according to their protein compositions. It was shown that ribosomal protein composition is a useful characteristic for studies of bacterial taxonomy.

Erythromycin-resistant mutant of Escherichia coli with altered ribosomal protein component

Erythromycin combines with 50S ribosomal subunit of an erythromycin-sensitive Escherichia coli (strain Q13), while ribosomes from an erythromycin-resistant mutant from this strain have little affinity for the antibiotic. A protein component of the 50S subunit of the mutant strain is distinct from that of the parent Q13 strain.

Protein components in the 40s ribonucleoprotein particles in Escherichia coli

The 40S ribonucleoprotein particle in Escherichia coli cells, accumulated in the presence of a low concentration of chloramphenicol, lacks at least four ribosomal structural protein components which are present in the mature 50S ribosomal subunit. The 40S ribonucleoprotein prepared by exposing the 50S ribosomal subunit to a concentrated lithium chloride solution may also be deficient in the same protein components.