MATCH-UP/MATRIX: a microcomputer program designed to search for protein primary structure homology

MATCH-UP/MATRIX is a program designed to aid the investigatorinterested in determining primary protein structure. It is writtenin Applesoft BASIC for the Apple lle microcomputer. MATCH-UPwill survey any set of proteinaceous materials for amino acidsequence homology; however, it is primarily intended to comparethe structures of newly sequenced peptides with the establishedstructure of a protein with suspected homology. Any peptide-to-proteinalignment which shows a homology greater than or equal to thepercentage specified by the user will result in output. MATRIXwill compare the sequences of two proteins (peptides) in whateveralignment specified by the user and is intended to spot insertionsand/or deletions between structures. Received on December 2, 1985; accepted on March 10, 1986     

Asthma mortality: comparison between New Zealand and England.

Causes for the high mortality from asthma in New Zealand were investigated by comparing deaths from asthma in caucasian subjects aged 15-64 in New Zealand with those from asthma in the same age group in two regions in England. There were no significant differences in the accuracy of death certification. The verified asthma mortality in New Zealand (4.2/100,000) was over twice that in England. Many characteristics of patients and management, including poor compliance with treatment and deficiencies in long term and emergency care, were qualitatively similar in the two countries. New Zealand had an apparently higher rate of non-preventable deaths from asthma, suggesting a greater severity of asthma in New Zealand. In both countries, however, most deaths were associated with poor assessment, underestimation of severity and inappropriate treatment (over-reliance on bronchodilators and underuse of systemic corticosteroids), and delays in obtaining help. A greater frequency of some of these deficiencies in management remains a possible additional explanation for part of the excess mortality in New Zealand.     

Quantitative studies of postnatal changes in synapses in rat superficial motor cerebral cortex

Summary Quantitation of synapses at different postnatal ages has been undertaken in the cerebral cortex of the rat. In this study axial ratios of presynaptic bags, proportion of cortex occupied by presynaptic bags and numbers of synapses per unit volume of cortex have been estimated. Observations on synaptic vesicle packing densities have also been made.Synaptic bags become increasingly spherical up to 7 days of age and become more elongated thereafter. The proportion of cortex occupied by presynaptic bags increases rapidly up to 7 days of age and then at a decelerated rate up to maturity. The number of synapses per unit volume increases slowly over the first four days after which there is a rapid increase to 14 days, followed by a decelerated rate.The average presynaptic bag shows marked changes in volume with increasing age which indicate the probability of two stages of synaptic development. This two stage development is further reflected in the estimates on vesicle packing densities. The implications of the results are discussed in relationship to changes in functional activity of the cortex during postnatal development.The authors wish to express their thanks to Mr. R. Birchenough and Mr. J. Manston for much technical assistance.     

Incidence of pathogenic bacteria in raw milk in Ireland.

Raw milk from 70 farms was sampled over 13 months for salmonellas, listerias, Escherichia coli, Staphylococcus aureus and mastitic streptococci; total bacterial counts (TBC), coliforms and somatic cells were also counted. TBC < or = 30,000/ml were obtained in 63% of samples. High count milks were found mainly during the winter months: 13% of samples had > 10(4) mastitis pathogens/ml of milk. The mean somatic cell count varied from 4.0 x 10(5) to 8.0 x 10(5)/ml throughout the year with highest counts during the late lactation period. Coliforms were present in all samples, but 65-71% of samples had < 100 coliforms/ml. Up to 60% of supplies had < or = 10 E. coli/ml. One of the 589 samples tested (0.1%) was positive for salmonellas. Yersinia enterocolitica and Y. enterocolitica-like organisms were isolated from 39% of samples with up to 68% of samples positive at some sampling periods. A total of 222 strains of yersinias were isolated; Y. enterocolitica (59%) was the most common strain followed by Y. fredriksenii (35%), Y. kristensenii (1.0%), Y. intermedia (4.5%) and Y. aldovae (0.5%). Listerias were isolated from 8.3% of samples tested; 4.9% were Listeria monocytogenes and 3.4% were L. innocua. There was a significant rise in the isolation rate between December and April from a base line of 0-5% during the spring and summer to 35-37% during the winter months while the cows were indoors. Of 66 silage samples tested from the farms involved in the survey 9% of samples were positive for listerias; 3% of these were L. monocytogenes and 6% were L. innocua.(ABSTRACT TRUNCATED AT 250 WORDS)     

Quantitation and characterization of thyrotropin-releasing hormone in vagal nuclei and other regions of the medulla oblongata of the rat

Abstract: Since evidence is now available to support a nonendocrine autonomic function for thyrotropin-releasing hormone (TRH), quantitative measurements of TRH were made in nuclei of the vagal complex and other areas of the caudal medulla oblongata of the rat. Regions containing the dorsal motor nucleus of the vagus (DMN), nucleus tractus solitarius (NTS), hypoglossal nucleus, dorsal column nuclei, descending nucleus V (DNV), nucleus ambiguus (NA), raphe nuclei (MR) dorsomedial and ventromedial reticular formation, and inferior olivary nuclei were isolated from 300-μm-thick frozen sections of medulla by the micropunch technique. Each region was pooled bilaterally, homogenized in 0.1 M HCl, and vacuum-dried. Extracts were assayed for TRH by specific radioimmunoassay (RIA). TRH levels varied 100-fold among medulla nuclei. Highest content (ng/mg protein ± SEM) was found in DMN (14 ± 1.38) and NTS (4.7 ± 0.68), whereas lowest levels occurred in the DNV and MR (0.13, 0.06). Nearly 65% of the total medullary TRH was localized in nuclei associated with vagal complex (DMN, NTS, NA). Characterization of tissue immunoreactivity (TRHi) in these regions suggests the presence of TRH, since (1) medullary tissue extracts competed with ¹²⁵I-TRH for antibody binding sites with the same affinity as authentic TRH; (2) TRHi in tissue extracts co-migrated with synthetic TRH when subjected to reverse-phase high performance liquid chromatography and Sephadex G-10 chromatography; and (3) rat serum TRH peptidases degraded TRHi and authentic TRH at similar rates. Another group of rats was subjected to unilateral (right side) vagotomy. At 33 weeks post-vagotomy, the vagal preganglionic cell population in the ipsilateral DMN was depleted 50–75%, while the contralateral side was unaffected. Interestingly, the content of TRH in the ipsilateral (right) DMN remained unchanged, whereas TRH in the contralateral DMN increased by 50%. In contrast, TRH was significantly elevated in the NA on the ipsilateral side of the lesion. TRH in both ipsi- and contralateral NTS was unchanged when compared with sham-operated controls. These results indicate that (1) TRH is present in several specific loci of the medulla; (2) very high levels are found in the vagal complex; and (3) vagotomy may alter TRH in the contralateral DMN and ipsilateral NA.     

Origin of human chromosome 2 revisited

Similarities in chromosome banding patterns and hornologies in DNA sequence between chromosomes of the great apes and humans have suggested that human chromosome 2 originated through the fusion of two ancestral ape chromosomes. A lot of work has been directed at understanding the nature and mechanism of this fusion. The recent availability of the human chrornosome-2-specific alpha satellite DNA probe D2Z and the human chromosome-2p-specific subtelomeric DNA probe D2S445 prompted us to attempt cross-hybridization with chromosomes of the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) to search for equivalent locations in the great apes and to comment on the origin of human chromosome 2. The probes gave different results. No hybridization to the chromosome-2-specific alpha satellite DNA probe was observed on the presumed homologous great ape chromosomes using both high-stringency and low-stringency post-hybridization washes, whereas the subtelomeric-DNA probe specific for chromosome 2p hybridized to telomeric sites of the short arm of chromosome 12 of all three great apes. These observations suggest an evolutionary difference in the number of alpha satellite DNA repeat units in the equivalent ape chromosomes presumably involved in the chromosome fusion. Nevertheless, complete conservation of DNA sequence of the subtelomeric repeat sequence D2S445 in the ape chromosomes is demonstrated.     

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

Background

High-throughput sequencing has enabled detailed insights into complex microbial environments, including the human gut microbiota. The accuracy of the sequencing data however, is reliant upon appropriate storage of the samples prior to DNA extraction. The aim of this study was to conduct the first MiSeq sequencing investigation into the effects of faecal storage on the microbiota, compared to fresh samples. Culture-based analysis was also completed.

Methods

Seven faecal samples were collected from healthy adults. Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction. Sequencing was completed on the Illumina MiSeq platform. Culturing of total aerobes, anaerobes and bifidobacteria was also completed.

Results

No significant differences at phylum or family levels between the treatment groups occurred. At genus level only Faecalibacterium and Leuconostoc were significantly different in the fresh samples compared to the snap frozen group (p = 0.0298; p = 0.0330 respectively). Diversity analysis indicated that samples clustered based on the individual donor, rather than by storage group. No significant differences occurred in the culture-based analysis between the fresh, snap or -80°C frozen samples.

Conclusions

Using the MiSeq platform coupled with culture-based analysis, this study highlighted that limited significant changes in microbiota occur following rapid freezing of faecal samples prior to DNA extraction. Thus, rapid freezing of samples prior to DNA extraction and culturing, preserves the integrity of the microbiota.