Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification

Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.

307 THE FEASIBILITY OF USING AN INCLINOMETER TO PROVIDE OLDER HOSPITALISED PATIENTS WITH FEEDBACK ON THEIR ACTIVITY LEVELS

Background

Low levels of physical activity in older adults are well documented and have been associated with functional decline, acute sarcopenia, prolonged length of stay and higher readmission rates. Interventions to modify behaviour in hospitalised older adults include providing feedback on performance. Commercially available activity trackers and pedometers which rely on step count, are often unable to detect steps at the walking speeds found in older hospitalised patients. This study investigated the feasibility of using an inclinometer to measure the time spent by older hospitalised adults in lying and sitting versus standing and walking, and to provide feedback to patients on their active versus sedentary levels.

Methods

This was a feasibility study using a cross-sectional single centre design. Twelve inpatients over 70 years of age were fitted with an ActivPAL accelerometer on their thigh, which was worn continuously for 3 days. A graphic display of sedentary versus active time was provided to the participants each morning. Acceptability of wearing the device and receiving feedback was determined using a modified technology acceptance questionnaire.

Results

Twelve hospitalised older adults (7 female, 5 male) were included in the study, median age 74 (66-84). A modified technology questionnaire showed that 83% of participants found the ActivPAL device comfortable to wear, 100% reported that the feedback from the device was clear and understandable and 92% reported that the information enhanced their motivation for physical activity and that they would wear the device again.

Conclusion

This feasibility study shows that the ActivPAL is a device that can be worn in the hospital setting to provide older adults with feedback on their activity levels in order to modify behaviour and increase their levels of physical activity while in hospital.

137 VIRTUAL CONSULTATIONS IN GERIATRIC MEDICINE OUTPATIENT DEPARTMENTS; THE PERSPECTIVE OF GERIATRIC MEDICINE SPECIALIST TRAINEES

Background

Covid-19 social distancing measures restricted access to outpatient services. “Virtual Clinics”(VCs) were introduced in Outpatients Departments (OPDs) to continue service provision. OPD experience is vital to geriatric medicine training. The geriatric medicine Higher Specialist Training (HST) curriculum requires annual OPD participation. This study sought to identify the impact of VCs on geriatric medicine training.

Methods

An online mixed-method questionnaire was developed and circulated among geriatric medicine specialist trainees. 20 closed-questions collected demographic information and considered opinion of VCs. 5 open-questions enabled respondents to expand views of VCs. Closed-questions responses underwent quantitative descriptive analysis. Open-question responses underwent qualitative thematic analysis.

Results

Response rate was 61.4%. 86.3% reported VCs were conducted via telephone calls. 58% didn't feel comfortable conducting VCs. 64.7% didn't feel VCs positively contributed to training. 90.2% stated Face-To-Face (FTF) clinics offer greater training opportunities. 74.51% stated they were less likely to discuss VCs with consultants(compared to FTF clinics). 98.04% hadn't received training in conducting VCs. Qualitative analysis revealed four main themes: (1) Patient Selection: certain patient cohorts are unsuitable for VCs. VCs are useful in relaying simple results; not for patients with complex needs; (2) Practical Considerations: there must be access to required technologies for patients and medical staff. Medicolegal concerns were raised by several respondents; (3) Patient Care: the inability to examine patients is a challenge which impacts patient care. The lack of non-verbal cues impeded communication; (4) Training Impact: Respondents felt VCs weren't beneficial to training. There was a sense that training opportunities had been missed.

Conclusion

This study found high rates of dissatisfaction with VCs among geriatric trainees. This may be due to: (1) Inadequate training/preparation; (2) Inappropriate patient selection or (3) Lack of video-conferencing technologies. There is a sense that VCs have negatively impacted geriatric medicine training. Current policy advocates for the continuation of VCs. If VCs continue, additional resources may be needed to address any accompanying training deficit.

295 SPEP IT UP! DEVELOPING AN ALGORITHM FOR ABNORMAL SERUM PLASMA ELECTROPHORESIS RESULTS IN HIP FRACTURE PATIENTS

Background

Hip fracture is a common manifestation of osteoporosis. All patients who sustain a hip fracture should receive a specialist bone health assessment, including Serum Protein Electrophoresis (SPEP) because plasma cell disorders such as multiple myeloma are an important differential diagnosis. SPEP results can be challenging to interpret without training and expertise. We aimed to review the proportion of abnormal SPEP results in hip fracture patients and used a newly developed algorithm to assess urgency of referral to haematology.

Methods

The Orthogeriatrics and Haematology teams collaborated to develop an algorithm to help facilitate decision making in hip fracture patients with abnormal SPEP results. A retrospective study was then conducted using data from the local Hip Fracture Database from Quarters 1 and 3 in 2020, and the hospital electronic laboratory system. The algorithm was used to retrospectively determine which patients warranted haematology review. The electronic appointment system was then accessed to review whether those who warranted haematology referral had appointments on the system.

Results

Of 270 hip fracture presentations, 19 duplicate records were excluded. Five patients had no data and three patients had passed away. Of the remaining 243 patients, 193 (79.42%) had SPEP’s sent. Abnormalities were detected in 116 patients (47.74%). According to the SPEP referral pathway, two patients warranted routine referral and one patient required an urgent referral, none of whom appeared to have been referred to haematology. Two patients who did not warrant haematology referral were already under haematology for different conditions.

Conclusion

Not all patients who sustain acute osteoporotic fractures with an abnormal SPEP result require haematology referral. The need for an urgent or routine haematology can be guided by the SPEP result along with other clinical features. With the introduction of this pathway, it is proposed that all hip fracture patients will be triaged in a timely, appropriate, and consistent manner.

286 PERCEPTIONS OF RESEARCH AMONGST OLDER ADULTS

Background

Older adults are often excluded from healthcare research, particularly those with cognitive impairment. It is crucial that study participants have given informed consent and partake in research of their own free will. People with cognitive impairment are not always able to engage in the informed consent process. This can lead to under-representation of this cohort in studies. Understanding older people’s perceptions of research is important to better design policies and research studies that are inclusive of older adults. This pilot study aimed to gain a better understanding of older adults’ views about healthcare research and what they imagine their wishes would be if they were unable to consent themselves due to memory problems.

Methods

In this prospective observational study, participants were recruited from outpatient clinics. Consenting participants were surveyed over the phone to ascertain their perceptions of healthcare research.

Results

Twenty-five interviews were conducted. Median age was 76.24 years (range 68-85 years). Most respondents reached at least second level education (80%), and most volunteered knowing very little about healthcare research. All participants had a nominated next of kin. Of 23 participants who had not previously been involved in healthcare research, none had been asked to do so.

Most participants would be interested or very interested in participating in research if the study involved either survey questions (64%), chart review (88%), or additional investigations (68%), however only a minority were interested or very interested in partaking in research involving a trial drug (16%). Most participants (88%) would be happy or very happy for their next of kin to ‘consent’ on their behalf (if they themselves were unable to do so).

Conclusion

In this study, older adults had clear views about healthcare research and a keenness to participate. This group of older adults expressed trust in their next of kin to make decisions on their behalf regarding research participation. More research is required to explore this area further.

103 ORTHOGERIATRIC SERVICES IN THE FACE OF COVID-19

Background

Nationally agreed standards improve the level of care delivered to all older, frail, multi-morbid patients presenting with hip fractures. Dedicated Orthogeriatric services allow for these standards to be achieved in a multi-disciplinary team (MDT) setting. As the COVID-19 pandemic reached our shores, the model of care set out by the Irish Hip Fracture Standards (IHFS) was under threat. Our dedicated Orthopaedic Trauma ward became an acute COVID ward and the Orthogeriatric service was re-deployed to acute medicine for Quarter 2.

Methods

Using the Irish Hip Fracture Database, local data was analysed and compared with national data from Quarter 1 to 4 (Q1–4) in 2020.

Results

When comparing local IHFS’s with national figures, ongoing challenges and future goals are highlighted.

In 2020, there were 222 hip fracture patients (mean age 81.8 years) in our hospital. Standard 1, time to the ward <4 hours, stands at 71% locally (national average 33%). Standard 2, time to theatre <48 hours, is an ongoing challenge and remains at 66% (national average 75%). Standard 3, pressure ulcer rate, was the same as the national average at 3%. Standards 4, 5 and 6 in our hospital stand at 87% (national averages of 82%, 91% and 85% respectively).

In Q1, 56%, or over 1 in every 2 patients with hip fractures, met all of the Irish Hip Fracture Standards in our hospital. In Q2, only 18% of patients met all of the IHFS’s. Q3 saw improvements with 47% of all hip fracture patients achieving all IHFS’s. Q4 showed maintenance with 45% of all patients achieving all IHFS’s.

Conclusion

These findings highlight the need for a dedicated Orthogeriatric Service and Orthopaedic ward at all times. Going forward with the risk of future waves and the emergence of new variants, every effort should be made to maintain a comprehensive orthogeriatric service to minimise a negative impact on patient care.

MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated and upgraded since its last major renewal in 2014. Several curated datasets for intrinsic disorder and folding upon binding have been integrated from specialized databases. The indirect evidence has also been expanded to better capture information available in the PDB, such as high temperature residues in X-ray structures and overall conformational diversity. Novel nuclear magnetic resonance chemical shift data provides an additional experimental information layer on conformational dynamics. Predictions have been expanded to provide new types of annotation on backbone rigidity, secondary structure preference and disordered binding regions. MobiDB 3.0 contains information for the complete UniProt protein set and synchronization has been improved by covering all UniParc sequences. An advanced search function allows the creation of a wide array of custom-made datasets for download and further analysis. A large amount of information and cross-links to more specialized databases are intended to make MobiDB the central resource for the scientific community working on protein intrinsic disorder and mobility.

The application of machine learning to the modelling of percutaneous absorption: an overview and guide

Machine learning (ML) methods have been applied to the analysis of a range of biological systems. This paper reviews the application of these methods to the problem domain of skin permeability and addresses critically some of the key issues. Specifically, ML methods offer great potential in both predictive ability and their ability to provide mechanistic insight to, in this case, the phenomena of skin permeation. However, they are beset by perceptions of a lack of transparency and, often, once a ML or related method has been published there is little impetus from other researchers to adopt such methods. This is usually due to the lack of transparency in some methods and the lack of availability of specific coding for running advanced ML methods. This paper reviews critically the application of ML methods to percutaneous absorption and addresses the key issue of transparency by describing in detail - and providing the detailed coding for - the process of running a ML method (in this case, a Gaussian process regression method). Although this method is applied here to the field of percutaneous absorption, it may be applied more broadly to any biological system.

Cryo-electron tomography of Marburg virus particles and their morphogenesis within infected cells

Several major human pathogens, including the filoviruses, paramyxoviruses, and rhabdoviruses, package their single-stranded RNA genomes within helical nucleocapsids, which bud through the plasma membrane of the infected cell to release enveloped virions. The virions are often heterogeneous in shape, which makes it difficult to study their structure and assembly mechanisms. We have applied cryo-electron tomography and sub-tomogram averaging methods to derive structures of Marburg virus, a highly pathogenic filovirus, both after release and during assembly within infected cells. The data demonstrate the potential of cryo-electron tomography methods to derive detailed structural information for intermediate steps in biological pathways within intact cells. We describe the location and arrangement of the viral proteins within the virion. We show that the N-terminal domain of the nucleoprotein contains the minimal assembly determinants for a helical nucleocapsid with variable number of proteins per turn. Lobes protruding from alternate interfaces between each nucleoprotein are formed by the C-terminal domain of the nucleoprotein, together with viral proteins VP24 and VP35. Each nucleoprotein packages six RNA bases. The nucleocapsid interacts in an unusual, flexible "Velcro-like" manner with the viral matrix protein VP40. Determination of the structures of assembly intermediates showed that the nucleocapsid has a defined orientation during transport and budding. Together the data show striking architectural homology between the nucleocapsid helix of rhabdoviruses and filoviruses, but unexpected, fundamental differences in the mechanisms by which the nucleocapsids are then assembled together with matrix proteins and initiate membrane envelopment to release infectious virions, suggesting that the viruses have evolved different solutions to these conserved assembly steps.

In silico protein motif discovery and structural analysis

A wealth of in silico tools is available for protein motif discovery and structural analysis. The aim of this chapter is to collect some of the most common and useful tools and to guide the biologist in their use. A detailed explanation is provided for the use of Distill, a suite of web servers for the prediction of protein structural features and the prediction of full-atom 3D models from a protein sequence. Besides this, we also provide pointers to many other tools available for motif discovery and secondary and tertiary structure prediction from a primary amino acid sequence. The prediction of protein intrinsic disorder and the prediction of functional sites and SLiMs are also briefly discussed. Given that user queries vary greatly in size, scope and character, the trade-offs in speed, accuracy and scale need to be considered when choosing which methods to adopt.

What do we know about how humans cough?

We review the evidence that activation of the cerebral cortex can lead to movements of the vocal folds and possibly to cough. Electrical stimulation of the motor cortex can cause movements of the vocal folds and vocalizatioin, but cough has not been reported. The motor pathways are via the nucleus ambiguous and possibly the nucleus retroambuigualis in the brainstem. In humans, activation of the cerebral cortex by transcranial magnetic stimulation can cause motor potentials in the intrinsic laryngeal muscles and corresponding surface potentials. The relationships between the cortical sensation related to cough, the voluntary control of cough and the involvement of reflex pathways remain to be clarified.

Hierarchical classification with a competitive evolutionary neural tree

A new, dynamic, tree structured network, the Competitive Evolutionary Neural Tree (CENT) is introduced. The network is able to provide a hierarchical classification of unlabelled data sets. The main advantage that the CENT offers over other hierarchical competitive networks is its ability to self determine the number, and structure, of the competitive nodes in the network, without the need for externally set parameters. The network produces stable classificatory structures by halting its growth using locally calculated heuristics. The results of network simulations are presented over a range of data sets, including Anderson's IRIS data set. The CENT network demonstrates its ability to produce a representative hierarchical structure to classify a broad range of data sets.

T-cell recognition of mycobacterial GroES peptides in Thai leprosy patients and contacts

We report here the mapping of T-cell-stimulatory determinants of the GroES 10-kDa heat shock protein homologues from Mycobacterium leprae and Mycobacterium tuberculosis, which are known as major immunogens in mycobacterial infections. Peripheral blood mononuclear cells (PBMC) from treated tuberculoid leprosy or lepromatous leprosy patients and from healthy household or hospital staff contacts of the patients were cultured with 20 16-mer peptides covering the entire sequences of both M. leprae and M. tuberculosis GroES. The total number of recognized peptides was found to be the largest in family contacts, while responder frequencies to the individual tested peptides varied (5 to 80%) with specificity between the patient and contact groups. Proliferative responses to some peptides showed positive or negative associations of low statistical significance with DR and DQ alleles, though responses to most GroES peptides were genetically permissive. Notably, the sequence of the 25-40 peptide of M. leprae, but not that of M. tuberculosis, was more frequently stimulatory in tuberculoid leprosy patients than in either group of sensitized healthy contacts. This peptide bound to a number of HLA-DR molecules, of which HLA-DRB5*0101 had the strongest affinity. The epitope core binding to this allele was localized to the 29-to-37 sequence, and its key residue was localized to the M. leprae-specific glutamic acid at position 32. This epitope may be of interest for the development of a blood test- or skin test-based diagnostic reagent for tuberculoid leprosy, subject to further clinical evaluation in untreated patients.

Measurement of cytotoxic T lymphocyte precursor frequencies reveals cryptic HLA class I mismatches in the context of unrelated donor bone marrow transplantation

BACKGROUND

In this large, two-center study, 260 cytotoxic T lymphocyte precursor (CTLp) frequency assays, performed to assess patient-donor compatibility, were analyzed in relation to the degree of HLA matching.

METHODS

While the tissue-typing techniques used at the Royal Postgraduate Medical School (RPMS) and Anthony Nolan Bone Marrow Trust (ANBMT) differ, the results of the analyses on the two sites are analogous, with high CTLp frequencies (>1:100,000) in 42% and 41% of recipient-donor pairs, respectively.

RESULTS

Recipient-donor combinations with class I mismatches and class II identity were associated with high CTLp frequencies (collectively 83% vs. 17% low CTLp). This correlation was not as strong in pairs where class II mismatches were demonstrated (61% high vs. 39% low). Despite using different matching procedures, the RPMS and ANBMT both show that 32% of the "perfectly" matched pairs (i.e., where no mismatch was detected by any of the techniques used here) had high frequencies of recipient-specific CTLp.

CONCLUSIONS

The failure of conventional methods to identify such a level of histoincompatibilities indicates that the CTLp assay has an important role in the selection of unrelated donors for bone marrow transplantation.

The development of anti-HLA antibodies in multiply transfused preterm infants

The development of antihuman leucocyte antigen antibodies (aHLAA) in response to multiple transfusions in preterm infants was studied prospectively. Fifty seven infants requiring a minimum of two blood transfusions were recruited after obtaining informed written parental consent. They were randomised to receive either whole blood or blood that had been passed through a leucocyte filter. Anti-HLAA were sought in maternal and cord blood so as to ensure that any aHLAA detected after transfusion had not been passively transferred antenatally, and in 1 ml samples drawn monthly from the baby, at least 10 days from a previous transfusion, until discharge from hospital. Anti-HLAA were detected by microlymphocytotoxicity assay. Results were obtained in 42 babies, 19 in the filter and 23 in the no filter group. Fifteen babies had to be excluded because of protocol violation or because they died. None of the babies receiving filtered blood developed aHLAA, but seven babies in the no filter group developed aHLAA. In conclusion, multiply transfused preterm infants have the ability to elaborate antibodies to HLA and leucocyte filters may prevent this.

Transjugular liver biopsy: a review of 200 biopsies

Transjugular liver biopsy was performed in 200 patients for whom percutaneous biopsy was contraindicated because of coagulation disorders (36%), ascites (32%) or for the work-up of portal hypertension (32%). An adequate biopsy allowing a histological diagnosis was obtained in 155 patients (77%). The biopsy was inadequate in 13 patients (6.5%). In 32 patients (16%) the biopsy failed. Complications occurred in 18 patients (9%). Twelve (6%) patients developed liver capsule perforations which were immediately embolized without complication. Inadvertent carotid artery puncture and supraventricular tachycardias occurred in three patients each. Transjugular liver biopsy is a valuable technique which provides information which would otherwise be unavailable in those patients for whom percutaneous biopsy is considered unsafe.

Multiple sclerosis and HLA: is the susceptibility gene really HLA-DR or -DQ?

Seventy-one patients with multiple sclerosis (MS) were classified into four subgroups according to the clinical pattern of their disease; their HLA-DR and DQ polymorphisms were defined by serological methods and analysis of Taq1 digestion fragments hybridizing with DRB, DQA, and DQB cDNA probes. The frequencies of the polymorphisms in the patients were compared with those of 100 control subjects. The frequencies of a 3.25-kb fragment from Mspl digests of genomic DNA which hybridized to DQA were also defined in the same groups of patients and control subjects. HLA-DR2 (DRw 15 subtype) and the associated HLA-DQw6 were observed in significant excess in the patients compared with the normal subjects (63% vs. 32% for DRw15; 65% vs. 42% for DQw6). There were no significant differences in the distribution of the DR or DQ alleles between the groups of patients showing different clinical patterns of disease, nor was there an excess in the patients of DQw8 and DQw9 which share hypervariable region sequences of the DQB chain in common with DQw6. The results argue against two recently proposed hypotheses of MS. First, they are not consistent with the proposal that susceptibility to MS is associated with expression of a hypervariable region of DQB shared by DQw6, 8, and 9. Second, they do not support the concept that primarily chronic progressive and relapsing/remitting MS are two immunogenetically distinct disease entities. Our evidence is consistent with the hypothesis that one of the true disease susceptibility genes for MS lies elsewhere within the HLA region and in Northern European populations is found in significant association with DRw15 and DQw6.

Lupus erythematosus profundus with partial C4 deficiency responding to thalidomide

A female patient with disfiguring lupus erythematosus profundus (LEP) from the age of 13 years was found to have an isolated partial C4 deficiency, with reduced levels of both allotypes, C4A and C4B. A genetic basis for the hypocomplementaemia was confirmed by a family study of complement and HLA types which revealed heterozygous null alleles for C4A and C4B in the proband. Marked improvement in her cutaneous lesions occurred with thalidomide.

Family study of the major histocompatibility complex in HLA DR3 negative patients with systemic lupus erythematosus

Susceptibility to systemic lupus erythematosus (SLE) is known to be governed by genes in the HLA region of the 6th chromosome. From previous studies it has not been possible to distinguish between the effects of null genes for the complement component C4 and HLA-DR3, because of the marked linkage disequilibrium between DR3 and a null allele of C4A (C4A QO) in caucasoid populations. We report here an immunogenetic study of 44 cases of SLE, selected because they were DR3 negative. Eighteen of the 30 Caucasoid cases (60%) had extended HLA haplotypes with a C4 null allele, compared with 22 of 60 (37%) of a control panel of 60 DR3 negative normal Caucasoid subjects. This difference is significant (chi 2 = 4.41; 0.05 greater than P greater than 0.01). Of 14 non-caucasoid patients analysed, 10 had a C4 null allele. It is concluded that the null alleles of the C4 A and B genes are themselves directly responsible for conferring susceptibility to SLE.