Whole protein sequencing and quantification without proteolysis, terminal residue cleavage, or purification: A computational model

Sequencing and quantification of whole proteins in a sample without separation, terminal residue cleavage, or proteolysis are modeled computationally. Similar to recent work on DNA sequencing (PNAS 113, 5233-5238, 2016), a high-volume conjugate is attached to every instance of amino acid (AA) type AAi, 1 ≤ i ≤ 20, in an unfolded whole protein, which is then translocated through a nanopore. From the volume excluded by 2L residues in a pore of length L nm (a proxy for the blockade current), a partial sequence containing AAi is obtained. Translocation is assumed to be unidirectional, with residues exiting the pore at a roughly constant rate of ~1/μs (Nature Biotechnology 41, 1130-1139, 2023). The blockade signal is sampled at intervals of 1 μs and digitized with a step precision of 70 nm3; the positions of the AAis are obtained from the positions of well-defined quantum jumps in the signal. This procedure is applied to all 20 standard AA types, the resulting 20 partial sequences are merged to obtain the whole protein sequence. The complexity of subsequence computation is O(N) for a protein with N residues. The method is illustrated with a sample protein from the human proteome (Uniprot id UP000005640_9606). A mixture of M' protein molecules (including multiple copies) can be sequenced by constructing an M' × 20 array of partial sequences from which proteins occurring multiple times are first isolated and their sequences obtained separately. The remaining M singly-occurring molecules are detected from M disjoint paths through the 20 columns of the reduced M × 20 array. Detection complexity is O(M20), which is nominally in polynomial time but practical only for small M; to use this method a sample may be subdivided into subsamples down to this level. Quantification of proteins can be done by sorting their computed sequences on the sequence strings and counting the number of duplicates. The possibility of translating this procedure into practice and related implementation issues are discussed.

Identifying residues in unfolded whole proteins with a nanopore: a theoretical model based on linear inequalities

A theoretical model is proposed for the identification of individual amino acids (AAs) in an unfolded whole protein's primary sequence. It is based in part on a recent report (Nat. Biotech. 41, 1130-1139, 2023) that describes the unfolding and translocation of whole proteins at constant speed through a biological nanopore (alpha-Hemolysin) of length 5 nm with a residue dwell time inside the pore of ~10 μs. Here current blockade levels in the pore due to the translocating protein are assumed to be measured with a limited precision of 70 nm3 and a bandwidth of 20 KHz for measurement with a low-bandwidth detector. Exclusion volumes in two pores of slightly different lengths are used as a computational proxy for the blockade signal; subsequence exclusion volume differences along the protein sequence are computed from the sampled translocation signals in the two pores relatively shifted multiple times. These are then converted into a system of linear inequalities that can be solved with linear programming and related methods; residues are coarsely identified as belonging to one of 4 subsets of the 20 standard AAs. To obtain the exact identity of a residue an artifice analogous to the use of base-specific tags for DNA sequencing with a nanopore (PNAS 113, 5233-5238, 2016) is used. Conjugates that add volume are attached to a given AA type, this biases the set of inequalities toward the volume of the conjugated AA, from this biased set the position of occurrence of every residue of the AA type in the whole sequence is extracted. By applying this step separately to each of the 20 standard AAs the full sequence can be obtained. The procedure is illustrated with a protein in the human proteome (Uniprot id UP000005640_9606).

A binary/digital approach to amino acid identification and its application to peptide sequencing and protein identification

A binary/digital method is proposed in theory for the identification of single amino acids (AAs) in the bulk or with a few molecules from a single binary measurement. Combined with Edman degradation (or other cleaving method), it can be used to sequence a peptide or identify the parent protein from a partial sequence. The approach is centered on the superspecificity property of transfer RNAs (tRNAs). Markedly different from conventional and recent single molecule (SM) sequencing methods based on analog measurements, it changes the analytical question 'Which AA is it?' to the much simpler one 'Is there an AA in the detection space?'. Each of 20 terminal residues cleaved from 20 copies of a peptide enters a different cavity with a unique tRNA; tRNA charging (or binding with AA) occurs only in the cavity with the cognate AA. The bound AA or the AA separated from the tRNA is detected with a single binary measurement; its identity is known from the position of the single high bit in the resulting 20-bit output. Alternatively, a 20-stage pipeline can be used with sparse samples. Detection of the bound AA can be done optically by tagging the AAs with a fluorescent dye, or of the freed AA electrically with a nanopore. Necessary conditions for accurate AA identification are satisfied in principle; related computations and simulation results are presented. A modified version that can be used for de novo sequencing in parallel of large numbers of peptides immobilized on a glass slide with the tRNAs carrying a fluorescent tag is also proposed. Both methods can be used for protein identification from partial sequences containing 2 or 3 AA types by using only the corresponding tRNAs. Experiments may be performed to validate them, followed by translation into practice with existing technology; potential implementation issues are discussed. Binary/digital amino acid identification for peptide sequencing.

Telomerase Reverse Transcriptase Promoter Mutations in A Cohort Of Adult Gliomas - Clinicopathological Correlates

BACKGROUND

Introduction: Gliomas were previously classified histologically, although now the latest WHO classification incorporates several molecular markers to classify these. Detection of TERT promoter mutations is assuming increased importance due to its relevance to prognostication.

OBJECTIVE

: The aim of this study was to determine the frequency of TERT promoter mutations, association of TERT promoter mutations with other molecular alterations and to assess the role of TERT promoter mutations in overall survival and progression-free survival in relation to histological and molecular glioma subtypes.

MATERIALS AND METHODS

This study analyzed a cohort of 107 adult patients with diffuse gliomas, WHO grades II and III and glioblastoma, by immunohistochemistry for IDH and ATRX mutations, FISH for 1p/19q co-deletions and PCR sequencing for TERT promoter mutation. Further, five glioma molecular sub-groups were derived using three molecular alteration and included the sub-groups with: i) IDH mutations only, ii) IDH and TERT mutations only, iii) IDH and 1p/19q co-deletion only, iv) Triple negative, and v) Triple positive.

RESULTS

IDH mutations and 1p/19q co-deletions were individually and significantly associated with an improved progression free (P = 0.001 and P = 0.002, respectively) and overall survival (P = 0.000 and P = 0.005, respectively) in the present cohort of gliomas. TERT promoter mutations occurred frequently in anaplastic oligodendrogliomas (94%), oligodendrogliomas (87.5%) and glioblastomas (54%). Sub-division into molecular sub-groups showed that the triple-positive tumors carried the best prognosis, followed by IDH only, triple negative and finally the TERT mutation only tumors (P < 0.000).

CONCLUSION

: This indicates that sub-classification using these molecular markers separates tumors into prognostically relevant categories.

Protein fingerprinting with digital sequences of linear protein subsequence volumes: a computational study

Proteins in a proteome can be identified from a sequence of K integers equal to the digitized volumes of subsequences with L residues from the primary sequence of a stretched protein. Exhaustive computations on the proteins of Helicobacter pylori (UniProt id UP000000210) with L and K in the range 4-8 show that approx. 90% of the proteins can be identified uniquely in this manner. This computational result can be translated into practice with a nanopore, an emerging technology that does not require analyte immobilization, proteolysis or labeling. Unlike other methods, most of which focus on a specific target protein, nanopore-based methods enable the identification of multiple proteins from a sample in a single run. Recent work by Kennedy, Kolmogorov and associates shows that the blockade current due to a protein molecule translocating through a nanopore is roughly proportional to one or more contiguous residues. The present study points to a modified version in which the volumes of subsequences (rather than of single residues) may be obtained by integrating the blockade current due to L contiguous residues. The advantages arising from this include lower detector bandwidth, elimination of the homopolymer problem and reduced noise. Because an identifier is based on near as well as distant (up to 2KL-L) residues, this approach uses more global information than an approach based on single residues and short-range correlations. The results of the study, which are available in a data supplement, are discussed in detail. Potential implementation issues are addressed.

Are sanitation interventions a threat to drinking water supplies in rural India? An application of tryptophan-like fluorescence

Open defecation is practised by over 600 million people in India and there is a strong political drive to eliminate this through the provision of on-site sanitation in rural areas. However, there are concerns that the subsequent leaching of excreta from subsurface storage could be adversely impacting underlying groundwater resources upon which rural populations are almost completely dependent for domestic water supply. We investigated this link in four villages undergoing sanitary interventions in Bihar State, India. A total of 150 supplies were sampled for thermotolerant (faecal) coliforms (TTC) and tryptophan-like fluorescence (TLF): an emerging real-time indicator of faecal contamination. Sanitary risk inspections were also performed at all sites, including whether a supply was located within 10 m of a toilet, the recommended minimum separation. Overall, 18% of water supplies contained TTCs, 91% of which were located within 10 m of a toilet, 58% had TLF above detection limit, and sanitary risk scores were high. Statistical analysis demonstrated TLF was an effective indicator of TTC presence-absence, with a possibility of TTCs only where TLF exceeded 0.4 μg/L dissolved tryptophan. Analysis also indicated proximity to a toilet was the only significant sanitary risk factor predicting TTC presence-absence and the most significant predictor of TLF. Faecal contamination was considered a result of individual water supply vulnerability rather than indicative of widespread leaching into the aquifer. Therefore, increasing faecal contamination of groundwater-derived potable supplies is inevitable across the country as uptake of on-site sanitation intensifies. Communities need to be aware of this link and implement suitable decentralised low-cost treatment of water prior to consumption and improve the construction and protection of new supplies.

A tandem cell for nanopore-based DNA sequencing with exonuclease

An electrolytic cell with two nanopores in tandem and an exonuclease in between can efficiently and accurately sequence a single strand of DNA.

Amino acid discrimination in a nanopore and the feasibility of sequencing peptides with a tandem cell and exopeptidase

Peptide sequencing in an electrolytic cell with two nanopores in tandem and exopeptidase.

Evaluation of safety and immunogenicity of HNVAC, an MDCK-based H1N1 pandemic influenza vaccine, in Phase I single centre and Phase II/III multi-centre, double-blind, randomized, placebo-controlled, parallel assignment studies

The clinical evaluation of the MDCK-based H1N1 pandemic influenza vaccine HNVAC in adults aged 18-65 years is reported. In the Phase I randomized, double-blind, placebo-controlled, single-centre study, 160 subjects were parallelly assigned 3:1 to vaccine:placebo groups (n=60:20) with both the aluminium hydroxide adjuvanted and non-adjuvanted vaccine formulations. A single dose of both the formulations containing 15 μg of haemagglutinin protein showed minimal adverse reactions, the most common of which were pain at injection site (11.67%) and fever (10.00%). Both formulations produced 74-81% seroprotection (SRP: titre of ≥40), 67-70% seroconversion (SRC: four-fold increase in titres between days 0 and 21), and a four-fold increase in geometric mean titres (GMT). Aluminium hydroxide did not have a significant effect either on immunogenicity or on reactogenicity. Nevertheless, based on its recognized positive effects on the stability and immunogenicity of many vaccines, and its marginal benefit in both pre-clinical and Phase I studies of HNVAC, alum adjuvanted HNVAC was further tested in a staggered Phase II/III randomized, double-blind, placebo-controlled, multi-centre study of 200 and 195 subjects, respectively, parallelly assigned 4:1 to adjuvanted vaccine and placebo groups. In these studies, the most common adverse reactions were pain at injection site (6.88% and 5.77% in Stage 1 and Stage 2, respectively) and fever (7.50% and 7.05%, respectively), and a single dose resulted in 87-90% SRP, 85-86% SRC, and a nearly six-fold increase in GMT, meeting or exceeding licensing criteria. It is concluded that HNVAC is safe and immunogenic to adults of 18-65 years.

An immunogenicity study of a newly introduced purified vero cell rabies vaccine (Abhayrab) manufactured in India

Purified Vero cell culture rabies vaccine "Abhayrab" manufactured by Human Biologicals Institute, Ooty, India was subjected for immunogenicity studies. Pre-exposure study was undertaken on 60 healthy volunteers (Group I) with vaccination on days 0, 7 and 21. A group of 75 patients of category II (Group II), 67 of category III (Group III) were given post-exposure prophylaxis and 88 patients of category III were administered with rabies immunoglobulins (Group IV) along with post-exposure prophylaxis as per World Health Organization (WHO) recommendations with a booster on day 90. The volunteers and patients vaccinated showed very few adverse side effects. The blood samples collected from volunteers (Group I) on days 14, 35 and 365 and patients (Group II-IV) on days 14, 30, 90 and 365 showed geometric mean titres (GMT) of >0.5 IU/ml. The study indicated new rabies vaccine manufactured in India was found to be safe and immunogenic.

Rabies post-exposure prophylaxis in malnourished children exposed to suspect rabid animals

Over half of the world's malnourished children live in Asia where more than 90% of reported human rabies deaths occur. In order to determine the effect of malnutrition on the immune response to rabies post-exposure prophylaxis (PEP), 45 children with moderate to severe protein energy malnutrition (PEM) who were exposed to potentially rabid animals were enrolled in a clinical trial. Patients received purified chick embryo cell rabies vaccine (PCECV) on days 0, 3, 7, 14 and 30. Blood was drawn on days 0, 14 and 30 and evaluated for the presence of rabies virus neutralizing antibody. All children that met the protocol criteria developed rabies virus neutralizing antibody titers above the acceptable level of 0.5 IU/mL by day 14 and no serious adverse events were reported. We conclude that children in this study that received four or five doses of rabies vaccine intramuscularly developed an acceptable immune response despite their severe degree of protein energy malnutrition.

A block coding method that leads to significantly lower entropy values for the proteins and coding sections of Haemophilus influenzae

A simple statistical block code in combination with the LZW-based compression utilities gzip and compress has been found to increase by a significant amount the level of compression possible for the proteins encoded in Haemophilus influenzae, the first fully sequenced genome. The method yields an entropy value of 3.665 bits per symbol (bps), which is 0.657 bps below the maximum of 4.322 bps and an improvement of 0.452 bps over the best known to date of 4.118 bps using Matsumoto, Sadakane, and Imai's lza-CTW algorithm. Calculations based on a compact inverse genetic code show that the genome has a maximum entropy of 1.757 bps for the coding regions, with a possibly lower actual entropy. These results hint at the existence of hitherto unexplored redundancies that do not show up in Markov models and are indicative of more internal structure than suspected in both the protein and the genome.

Bilateral ulnar nerve paralysis: an unreported complication of drug-induced extrapyramidal rigidity

OBJECTIVE

This case report describes a very unusual consequence of drug-induced extrapyramidal side effects.

CLINICAL PICTURE

The patient developed bilateral ulnar nerve paralysis.

TREATMENT

The treatment consisted of anticholinergic medication and physiotherapy.

OUTCOME

The patient made a complete recovery over a period of 8 months.

CONCLUSIONS

There is a need to ensure compliance with anticholinergic medication when using depot neuroleptic medication.

Rationalizing neuroleptic polypharmacy in chronic schizophrenics: effects of changing to a single depot preparation

This study investigated the effects of transferring patients on combined depot and oral neuroleptics to a single depot preparation; a secondary objective was to assess the effects of transferring patients from one depot neuroleptic to another. It was found that, whereas transferring from one depot preparation (flupenthixol) to another (fluphenazine) had no clear disadvantage for the patients, changing over from a combined oral and depot (fluphenazine) regimen to equivalent doses of depot alone resulted in an unacceptably high rate of relapse. The reasons for this may relate to either the unique pharmacokinetics of these drugs or subtle qualitative differences between them. It is suggested that caution is necessary whenever attempts are made to rationalize polypharmacy in schizophrenic patients.

Dexamethasone suppression test and response to antidepressant therapy in psychogeriatric patients

Senile dementia patients show a high incidence of abnormal Dexamethasone Suppression Test (DST) which has been suggested to reflect the presence of atypical or subclinical depression; this study was designed to test this hypothesis. Thirty-six patients, diagnosed as suffering from dementia and/or depression on the DSM-III criteria, participated in the study. They were divided into three groups. dementia (12), depression (12) and dementia with depression (12). The results indicated that although patients with depression alone responded well to antidepressant therapy, no improvement occurred in patients with dementia. Demented patients who had clinical depression also showed a poor response. The response to treatment was unrelated to the DST status of the patients. It is concluded that abnormal DST in dementia patients is not indicative of a masked affective state, and antidepressants have no place in the management of dementia patients who have a positive DST but no overt affective symptoms.

Oxypertine in tardive dyskinesia: a long-term controlled study

A 6-month, double-blind, placebo-controlled study of oxypertine in tardive dyskinesia is described. Results suggest that any beneficial effect noticed initially is not sustained. When this effect is compared with the time course of development of supersensitivity after neuroleptics as reported in the literature, it becomes apparent that the drug, despite its different mechanism of action, behaves like any other conventional neuroleptic. On the basis of the findings, the authors feel that all proposed anti-dyskinetic drugs should be subjected to longer, controlled trials to prove their clinical efficacy.

Radio receptor assay of serum neuroleptic levels in psychiatric patients

The radioreceptor assay for the measurement of neuroleptic drugs in serum has been used to study the relationship between dose and serum level in schizophrenic patients receiving these drugs. The assay was found to be reproducible and capable of detecting neuroleptics in the sera of patients receiving a range of both oral and depot drugs, with the exception of trifluoperazine spansules. Linear correlations were obtained between daily dose and serum level for each drug both in individual patients on different doses and between patients on a stable dose. Extrapyramidal side effects were related to the serum neuroleptic level within, but not between, patients. The assay may be of use in clinical practice, including the assessment of compliance or poor response to neuroleptics.

Insight and lithium compliance

In a study of lithium compliance in 35 patients with Manic Depressive Psychosis on prophylactic lithium it was found that insight into the nature of illness and drug compliance were unrelated.

A Theory of Spontaneous Pattern Generation and Learning

Spontaneous firing in neural nets can be processed and interpreted as patterns of behavior. Such patterns can be learned through learning mechanisms present in synapses. This implies that behavioral patterns can form without a stimulus if the spontaneous firing rates in a neural net are sufficiently high.

Lithium neurotoxicity at 'therapeutic' levels a case report

A case of a young manic patient who developed severe neurotoxicity when on lithium alone has been presented. Investigations did not reveal presence of any infection, electrolyte imbalance or rise in lithium level.The possibility of lithium producing neurotoxicity at therapeutic levels for as yet unknown reasons is pointed out. It is suggested that this element of risk be considered when starting lithium for therapy or prophylaxis of affective disorders.

Intra and extra erythrocyte lithium ion concentration ratios in manic patients

In a study RBC-Plasma lithium ratios in manic patients treated with lithium we found that lithium responders had higher lithium ratios than lithium non-responders. There was, however, no cut off value which could differentiate lithium responders from non-responders.