If Opportunity Knocks: Understanding Contextual Factors' Influence on Cognitive Systems

Central to the Research Domain Criteria (RDoC) framework is the idea that RDoC constructs, which vary dimensionally by individual, are heavily influenced by contextual factors. Perhaps chief among these contextual factors is structural opportunity - the quality of resources available to a child as they grow. The aim of this study is to understand the impact of access to opportunity during childhood on three central RDoC cognitive systems constructs: language, visual perception, and attention. These constructs were measured using clinical data from psychological evaluations of youth ages 4-18 years (N = 16,523; Mage = 10.57, 62.3% male, 55.3% White). Structural opportunity was measured using the geocoded Child Opportunity Index 2.0 (COI), a composite score reflecting 29 weighted indicators of access to the types of neighborhood conditions that help children thrive. Findings indicate that, controlling for demographic and socioeconomic factors, greater access to opportunity is associated with significantly stronger cognitive skills across all three constructs. However, opportunity uniquely explains the largest proportion of the variance in language skills (8.4%), compared to 5.8% of the variance in visual processing skills and less than 2% of the variance in attention. Further, a moderating effect of age was found on the relation between COI and language skills, suggesting that the longer children remain exposed to lower levels of opportunity, the lower their language skills tend to be. Understanding how opportunity impacts cognitive development allows clinicians to offer better tailored recommendations to support children with cognitive systems deficits, and will support policy recommendations around access to opportunity.

Concordance of the Adaptive Behavior Assessment System, second and third editions

BACKGROUND

Adaptive functioning is an important area of assessment with implications for differential diagnosis, educational placement, service eligibility and criminal sentencing. While periodic normative and content updates of adaptive functioning measures are necessary to keep measures relevant, knowledge of equivalence between versions is also required if adaptive measures are to be used to track the stability of adaptive functioning skills over time.

METHOD

This paper presents two studies that used between-group and within-group comparison designs to examine the equivalence of the second and third editions of the Adaptive Behavior Assessment System (ABAS) in a mixed clinical sample. In study 1, ABAS-2 scores for children assessed between 2014 and 2015 (n = 1036; mean age = 10.24, SD = 3.44) were compared with ABAS-3 scores for children assessed between 2015 and 2016 (n = 1291; mean age = 10.51, SD = 3.70). Study 2 examined a separate sample of clinically referred children (n = 572) for whom parent ratings had been obtained on both the ABAS-2 (mean age = 9.65, SD = 2.80) and ABAS-3 (mean age = 13.33, SD = 2.95) in the course of repeated assessment.

RESULTS

For Study 1, while no intelligence quotient score differences were observed between the ABAS-2 group (mean Verbal Comprehension Index = 93.67, SD = 16.95) and the ABAS-3 group (mean Verbal Comprehension Index = 93.08, SD = 17.42), ABAS-2 scores were lower than ABAS-3 scores on the Conceptual, Practical, and General Adaptive Composite scales. In study 2, a similar pattern was observed (ABAS-2 < ABAS-3 on the Conceptual, Practical, and General Adaptive Composite scales), and concordance correlation coefficients ranged from 0.54 [0.49, 0.58] (Practical composite) to 0.68 [0.64, 0.72] (Conceptual composite). The Practical composite had the lowest concordance correlation coefficient value and the largest mean score difference between ABAS versions.

CONCLUSIONS

The ABAS-3 scores may be higher than ABAS-2 scores in clinical populations. Knowledge of these potential discrepancies will be critical when interpreting standard score changes across ABAS versions in the course of clinical, educational and forensic assessments.

Caregiver Perspectives on Informed Consent for a Pediatric Learning Healthcare System Model of Care

BACKGROUND

Data is needed to provide insight into the issue of preference around consent for use of pediatric clinical data for research. This study evaluated caregivers' preferences concerning use of their child's clinical information.

METHODS

Caregivers of children (n = 101; response rate 81.5% of n = 124) presenting for psychological evaluation at an urban medical center viewed a video regarding how the information contained in their child's medical record could be used for research.

RESULTS

An anonymous survey following the video indicated that: 1) >90% of caregivers felt comfortable with their child's information being used; 2) >90% of caregivers felt their child's privacy would be adequately protected; 3) 98% of caregivers reported themselves to be as or more likely to return to the institution after viewing the video; 4) 60% of caregivers felt no additional consent procedures beyond viewing the video were needed, while 20% preferred an opt-out and 20% preferred a traditional consent procedure. Caregiver demographic variables were largely unrelated to consent preferences.

DISCUSSION

Overall, caregivers reported strong support for use of their child's clinical data for research purposes.

Executive functions among youth with Down Syndrome and co-existing neurobehavioural disorders

BACKGROUND

Executive function (EF) deficits are a recognised component of the cognitive phenotype of youth with Down Syndrome (DS). Recent research in this area emphasises the use of behaviour ratings, such as the Behavior Rating Inventory of Executive Functions-Preschool Version (BRIEF-P), to capture the real-world applications of executive functions. To account for the intellectual functioning of youth with DS, this measure is used out of age range; however, its psychometric properties when used in this fashion are unknown. The goals of this study are to evaluate psychometric characteristics of the BRIEF-P among youth with DS and to examine the pattern of EF strengths/weaknesses in children with DS and co-occurring psychiatric conditions.

METHOD

A total of 188 clinically referred youth with DS, ages 3-13 were rated by their caregivers using the BRIEF-P. These youth were evaluated by a clinician with expertise in DS and were characterised as having no co-occurring behavioural disorder (Typical DS group), co-occurring Autism Spectrum Disorder (DS + ASD) or co-occurring Disruptive Behaviour Disorder (DS + DBD).

RESULTS

An exploratory factor analysis of item-level BRIEF-P data from clinically referred youth with DS supported the theoretically derived three-factor structure originally proposed for the BRIEF-P (Emergent Metacognition, Flexibility and Inhibitory Self-Control); however, the item composition of each factor varied somewhat in comparison to the original structure of the measure. Group comparisons indicate that, while youth with typical DS evidence fewer executive function difficulties across all domains, youth with DS + ASD show the greatest weaknesses in Emergent Metacognition, and youth with DS + DBD show significant difficulties in both Emergent Metacognition and Inhibition.

CONCLUSIONS

These findings offer preliminary support for use of the BRIEF-P with clinically referred youth with Down Syndrome. Some scoring modifications may be necessary if the theoretically derived index scores are to be used with this population. BRIEF-P scores may offer an empirical basis for differentiating DS youth with varying behavioural profiles.

Structural and functional analysis of the origin of replication of mitochondrial DNA from Paramecium aurelia : I. Inverted complements form the terminal loop

Initiation of replication of the linear mitochondrial DNA from Paramecium occurs at a unique cross-linked terminus of the monomer molecule. Dimer length molecules, containing head-to-head monomers, are replicative intermediates. Previous studies have been with cloned dimer initiation region fragments but here we have isolated and sequenced isomeric forms of restriction fragments located at the initiation end of the monomer. The sequence isomers are inverted complements of each other in the region identified as the single-stranded DNA terminal loop. The unusual electrophoretic behaviour of these terminal restriction fragments supports the sequence data result that the loop is single stranded. These structural features are discussed in regard to mechanisms for the processing of dimer to monomer molecules.

tau binds and organizes Escherichia coli replication proteins through distinct domains: domain III, shared by gamma and tau, oligomerizes DnaX

The tau and gamma proteins of the DNA polymerase III holoenzyme DnaX complex are products of the dnaX gene with gamma being a truncated version of tau arising from ribosomal frameshifting. tau is comprised of five structural domains, the first three of which are shared by gamma (Gao, D., and McHenry, C. (2001) J. Biol. Chem. 276, 4433-4453). In the absence of the other holoenzyme subunits, DnaX exists as a tetramer. Association of delta, delta', chi, and psi with domain III of DnaX(4) results in a DnaX complex with a stoichiometry of DnaX(3)deltadelta'chipsi. To identify which domain facilitates DnaX self-association, we examined the properties of purified biotin-tagged DnaX fusion proteins containing domains I-II or III-V. Unlike domain I-II, treatment of domain III-V, gamma, and tau with the chemical cross-linking reagent BS3 resulted in the appearance of high molecular weight intramolecular cross-linked protein. Gel filtration of domains I-II and III-V demonstrated that domain I-II was monomeric, and domain III-V was an oligomer. Biotin-tagged domain III-V, and not domain I-II, was able to form a mixed DnaX complex by recruiting tau, delta, delta', chi, and psi onto streptavidin-agarose beads. Thus, domain III not only contains the delta, delta', chi, and psi binding interface, but also the region that enables DnaX to oligomerize.

Assembly of DNA polymerase III holoenzyme: co-assembly of gamma and tau is inhibited by DnaX complex accessory proteins but stimulated by DNA polymerase III core

Although the two alternative Escherichia coli dnaX gene products, tau and gamma, are found co-assembled in purified DNA polymerase III holoenzyme, the pathway of assembly is not well understood. When the 10 subunits of holoenzyme are simultaneously mixed, they rapidly form a nine-subunit assembly containing tau but not gamma. We developed a new assay based on the binding of complexes containing biotin-tagged tau to streptavidin-coated agarose beads to investigate the effects of various DNA polymerase III holoenzyme subunits on the kinetics of co-assembly of gamma and tau into the same complex. Auxiliary proteins in combination with delta' almost completely blocked co-assembly, whereas chipsi or delta' alone slowed the association only moderately compared with the interaction of tau with gamma alone. In contrast, DNA polymerase III core, in the absence of deltadelta' and chipsi, accelerated the co-assembly of tau and gamma, suggesting a role for DNA polymerase III' [tau(2)(pol III core)(2)] in the assembly pathway of holoenzyme.

A novel assembly mechanism for the DNA polymerase III holoenzyme DnaX complex: association of deltadelta' with DnaX(4) forms DnaX(3)deltadelta'

We have constructed a plasmid-borne artificial operon that expresses the six subunits of the DnaX complex of Escherichia coli DNA polymerase III holoenzyme: tau, gamma, delta, delta', chi and psi. Induction of this operon followed by assembly in vivo produced two taugamma mixed DnaX complexes with stoichiometries of tau(1)gamma(2)deltadelta'chipsi and tau(2)gamma(1)deltadelta'chipsi rather than the expected gamma(2)tau(2)deltadelta'chipsi. We observed the same heterogeneity when taugamma mixed DnaX complexes were reconstituted in vitro. Re-examination of homomeric DnaX tau and gamma complexes assembled either in vitro or in vivo also revealed a stoichiometry of DnaX(3)deltadelta'chipsi. Equilibrium sedimentation analysis showed that free DnaX is a tetramer in equilibrium with a free monomer. An assembly mechanism, in which the association of heterologous subunits with a homomeric complex alters the stoichiometry of the homomeric assembly, is without precedent. The significance of our findings to the architecture of the holoenzyme and the clamp-assembly apparatus of all other organisms is discussed.

Characterization of the unique C terminus of the Escherichia coli tau DnaX protein. Monomeric C-tau binds alpha AND DnaB and can partially replace tau in reconstituted replication forks

A contact between the dimeric tau subunit within the DNA polymerase III holoenzyme and the DnaB helicase is required for replication fork propagation at physiologically-relevant rates (Kim, S., Dallmann, H. G., McHenry, C. S., and Marians, K. J. (1996) Cell 84, 643-650). In this report, we exploit the OmpT protease to generate C-tau, a protein containing only the unique C-terminal sequences of tau, free of the sequences shared with the alternative gamma frameshifting product of dnaX. We have established that C-tau is a monomer by sedimentation equilibrium and sedimentation velocity ultracentrifugation. Monomeric C-tau binds the alpha catalytic subunit of DNA polymerase III with a 1:1 stoichiometry. C-tau also binds DnaB, revealed by a coupled immunoblotting method. C-tau restores the rapid replication rate of inefficient forks reconstituted with only the gamma dnaX gene product. The acceleration of the DnaB helicase can be observed in the absence of primase, when only leading-strand replication occurs. This indicates that C-tau, bound only to the leading-strand polymerase, can trigger the conformational change necessary for DnaB to assume the fast, physiologically relevant form.

Identification of the acidic residues in the active site of DNA polymerase III

The mechanism of nucleotide addition by DNA polymerases involves two metal ions that are coordinated in the active site by conserved acidic residues. The three acidic residues that chelate Mg2+ in the active site of Escherichia coli DNA polymerase III have been identified as Asp401, Asp403, and Asp555 by site-directed mutagenesis. Candidates for mutagenesis were initially chosen based on absolute conservation of acidic residues in an alignment of more than 20 diverse DnaE sequences. Conservative Asp to Glu mutations at positions 401 and 403 reduced the activities of the mutant polymerases 2000 and 333-fold, respectively, from that of the wild-type. The third carboxylate was identified by a series of mutations for each critical candidate. With the exception of Glu, all of the mutations at Asp555 led to severely diminished polymerase activity, while each of the other candidates exhibited several relatively active mutant polymerases. Moreover, only the identified active site mutant polymerases displayed a significant enhancement of activity in Mn2+ compared with Mg2+. These data suggest a direct involvement of the mutated amino acid in metal ion binding.

Attenuation of neurovirulence of Theiler's murine encephalomyelitis virus strain GDVII is not sufficient to establish persistence in the central nervous system

Virus recombinants constructed from Theiler's murine encephalomyelitis virus (TMEV) strain GDVII, which causes a rapidly fatal encephalitis in mice, and the less virulent BeAn, which persists in the murine central nervous system (CNS) and causes inflammatory demyelination, and a GDVII mutant deleted of 46 of 76 leader protein amino acids were analysed for virus persistence in the CNS. The two recombinant and mutant viruses principally contain GDVII sequences including the nucleotides encoding the polyprotein and 3' untranslated region. These viruses were found to replicate in the CNS of mice but they did not produce acute encephalitis or paralysis, i.e. they were attenuated in neurovirulence compared to the GDVII parent. More important, none of the viruses persisted in the mouse CNS nor caused chronic demyelination. Thus, attenuation of GDVII neurovirulence alone is not sufficient to establish TMEV persistence. This result is discussed in the context of a genomic determinant for persistence.

A determinant for central nervous system persistence localized in the capsid of Theiler's murine encephalomyelitis virus by using recombinant viruses

The demyelinating process in Theiler's murine encephalomyelitis virus (TMEV) infection in mice requires virus persistence in the central nervous system. Using recombinant TMEV assembled between the virulent GDVII and less virulent BeAn virus cDNAs, we now provide additional evidence supporting the localization of a persistence determinant to the leader P1 (capsid) sequences. Further, recombinant viruses in which BeAn sequences progressively replaced those of GDVII within the capsid starting at the leader NH2 terminus suggest that a conformational determinant requiring homologous sequences in both the VP2 puff and VP1 loop regions, which are in close contact on the virion surface, might underlie persistence.

Localization of the active site of the alpha subunit of the Escherichia coli DNA polymerase III holoenzyme

Using a deletion approach on the alpha subunit of DNA polymerase III from Escherichia coli, we show that there is an N-proximal polymerase domain which is distinct from a more C-proximal tau and beta binding domain. Although deletion of 60 residues from the alpha N terminus abolishes polymerase activity, deletions of 48, 169, and 342 amino acids from the C terminus progressively impair its catalytic efficiency but preserve an active site. Deletion of 342 C-terminal residues reduces k(cat) 46-fold, increases the Km for gapped DNA 5.5-fold, and increases the Km for deoxynucleoside triphosphates (dNTPs) twofold. The 818-residue protein with polymerase activity displays typical Michaelis-Menten behavior, catalyzing a polymerase reaction that is saturable with substrate and linear with time. With the aid of newly acquired sequences of the polymerase III alpha subunit from a variety of organisms, candidates for two key aspartate residues in the active site are identified at amino acids 401 and 403 of the E. coli sequence by inspection of conserved acidic amino acids. The motif Pro-Asp-X-Asp, where X is a hydrophobic amino acid, is shown to be conserved among all known DnaE proteins, including those from Bacillaceae, cyanobacteria, Mycoplasma, and mycobacteria. The E. coli DnaE deletion protein with only the N-terminal 366 amino acids does not have polymerase activity, consistent with the proposed position of the active-site residues.

Phonophoretic delivery of 10% hydrocortisone through the epidermis of humans as determined by serum cortisol concentrations

BACKGROUND AND PURPOSE

The purpose of this investigation was to determine whether application of hydrocortisone phonophoresis enhances transcutaneous delivery of topically applied hydrocortisone in humans, as determined by blood cortisol levels.

SUBJECTS

The subjects were 16 men and women, between the ages of 18 and 33 years (X = 25, SD = 2.74), without symptoms of any ongoing inflammatory condition.

METHODS

A gel coupling medium containing 10% hydrocortisone acetate was used. Ultrasound was delivered over a 50-cm2 area for 5 minutes at an intensity of 1.0 W/cm2 and a frequency of 1.0 MHz. Each subject received a control treatment (ultrasound alone) and an experimental treatment (hydrocortisone phonophoresis) on the volar aspect of the forearm 1 week apart. Blood was drawn, under both control and experimental conditions, from a cubital vein just proximal to the treatment site prior to each treatment and 0,5, and 15 minutes posttreatment. Serum cortisol concentrations were measured using a fluorescence polarization immunoassay.

RESULTS

No rise in serum cortisol concentrations following hydrocortisone phonophoresis was detected.

CONCLUSION AND DISCUSSION

These findings suggest that there was no penetration of hydrocortisone through the epidermis and into the underlying vasculature. Clinical implications regarding hydrocortisone levels within the subcutaneous tissues are discussed, and further research is suggested.

In vivo assembly of the tau-complex of the DNA polymerase III holoenzyme expressed from a five-gene artificial operon. Cleavage of the tau-complex to form a mixed gamma-tau-complex by the OmpT protease

A plasmid was constructed that encodes all five subunits of the Escherichia coli tau-complex on a single artificially constructed operon under the control of an inducible promoter. The proteins tau, delta, delta , chi, and psi overproduced from this artificial operon assemble efficiently in vivo, providing an efficient source of homogeneous tau-complex. The gamma subunit is a truncated form of tau that is produced by a translational frameshift. When protein expression was induced in bacterial strains containing the outer membrane protein T (OmpT) protease, tau was proteolyzed after lysis to a gamma-like protein, gammaP, and a peptide, C-tau, corresponding to the C terminus of tau. N-terminal sequencing of C-tau revealed a cleavage site between two lysines at positions 429 and 430 of tau. The deduced sequence of gammaP is, therefore, only two amino acids shorter than natural gamma. The proteolysis by OmpT was also shown directly by using purified OmpT and tau-complex in an in vitro reaction. A gammaP-complex and a mixed tau-gammaP-complex were purified from ompT+ cells. When the tau-complex proteins were overexpressed in ompT- bacteria, intact tau-complex lacking gammaP could be purified.

Assembly of Theiler's virus recombinants used in mapping determinants of neurovirulence

A major determinant of neurovirulence for the GDVII strain of Theiler's virus, a murine picornavirus, was mapped to the P1 capsid protein region. Chimeric viruses were constructed by using sequences from the 5' noncoding and P1 regions of the virulent GDVII strain to replace equivalent regions of the less virulent BeAn strain. Neurovirulence in mice progressively increased as larger regions of BeAn capsid protein-encoding sequences were replaced. The in vitro growth characteristics of the chimeras showed that some chimeras were growth delayed in BHK-21 cells even though the viral constructs exhibited larger plaque sizes, were less temperature sensitive, and were more thermally stable than BeAn. Examination of assembly intermediates revealed an altered pentamer conformation and delayed empty capsid formation for the growth-compromised viruses. For these constructs, their chimeric nature inadvertently resulted in virion assembly defects that complicated finer-scale mapping of the determinants of virulence within the capsid region. These results demonstrate the importance of determining in vitro growth characteristics of chimeras to correctly decipher the significance of their phenotypes. VP1 does not contain a complete determinate for virulence because a chimera with VP1-encoding sequences from GDVII in an otherwise BeAn virus has an attenuated phenotype but is not growth compromised in vitro. The source of sequences, BeAn or GDVII, in the 5' noncoding region had only slight effects on the virulence of recombinant constructs.

Nucleotide sequence identifies Vilyuisk virus as a divergent Theiler's virus

The Vilyuisk virus, originally thought to be the cause of a degenerative neurological disease of inhabitants of Siberia, has been characterized by sequence analysis of its 5' noncoding and coat protein coding regions. In the 5' noncoding, leader, and VP4 regions, the nucleotide identity between the sequences of known strains of Theiler's virus and Vilyuisk virus is about 90%. In the VP1-encoding region, the similarity drops to about 66% compared to the 50% similarity between sequences of Theiler's virus and encephalomyocarditis virus. Using the known crystal structure of one Theiler's virus strain, it is shown that the sequence heterogeneities generally occur at exposed surface residues. Vilyuisk virus is the most divergent Theiler's virus known. A tissue culture-adapted isolate has been propagated and found to exhibit low neurovirulence in CD-1 mice.

A single base deletion in the 5' noncoding region of Theiler's virus attenuates neurovirulence

Viral chimeras have been constructed through in vitro manipulations of the infectious cDNA clones of two prototypes of Theiler's murine encephalomyelitis virus: (i) the virulent GDVII strain and (ii) the less virulent BeAn and VL strains. Previous studies have suggested that the phenotypic differences in virulence between the BeAn and GDVII strains map to both the 5' noncoding and the coat protein regions of these viral genomes. It is shown here that attenuation mapped to the 5' noncoding region is due, at least in part, to an inadvertent deletion resulting from a cloning artifact of one C nucleotide out of four between positions 876 and 879 in the BeAn sequences. The in vitro growth characteristics in BHK-21 cells, however, do not reflect the large differences in neurovirulence between chimeras that are identical except for the deleted C. Another chimera with a mutation at position 877 and a deletion at 976 is also attenuated. The wild-type sequences from the less virulent strains BeAn and VL between nucleotides 1 and 933, in an otherwise GDVII chimera, do not attenuate virulence. Sequences of the 500 nucleotides of the 5' noncoding region proximal to the translation initiation codon were obtained for nine additional Theiler's virus strains. The attenuating deletions are discussed in the context of these sequences and the proposed secondary structures for the 5' noncoding region.

Possible insertion sequences in a mosaic genome organization upstream of the exotoxin A gene in Pseudomonas aeruginosa

Nucleotide sequence and Southern hybridization data revealed a mosaic genome organization in a region that extends several thousand base pairs upstream of the exotoxin A (toxA) gene in Pseudomonas aeruginosa. An interstrain comparison of DNA in this region showed a pattern of alternating segments of homologous and nonhomologous sequences. Two nonhomologous elements, approximately 1 kilobase pair upstream of the gene in strains PA103 and Ps388, were characterized in more detail. The sequence elements, denoted IS-PA-1 and IS-PA-2 for the different strains, are about 1,000 and 785 base pairs long, respectively, and have 5-base-pair direct repeats at their boundaries, consistent with their being DNA insertion sequences. The distribution of these elements in 34 different strains was determined. IS-PA-1 was found in a single copy upstream of toxA in half of the strains and was found in two copies in four of the strains. Some strains contained neither element, and one strain carried both. The genome of another strain, WR5, which lacks toxA, was shown to contain a 350-base-pair region that was highly homologous to DNA sequences located just upstream of toxA in other strains. The WR5 genome lacked several kilobase pairs of DNA that was found both upstream and downstream of this homologous region in the other strains.

Nucleotide sequence of the mitochondrial genome of Paramecium

The nucleotide sequence for 40,469 bp of the linear Paramecium aurelia mitochondrial (mt) genome is presented with the locations of the known genes, presumed ORFs, and their transcripts. Many of the genes commonly encoded in mt DNA of other organisms have been identified in the Paramecium mt genome but several unusual genes have been found. Ribosomal protein genes rps14, rps12, and rpl2 are clustered in a region that also contains two other genes usually found in chloroplasts, but rpl14 is over 16 kbp away. The ATP synthase gene, atp9, is encoded in this mt genome, but the atp6, atp8, and COIII genes have not been identified. All of the identified genes are transcribed. Many mono- and poly- cistronic transcripts have been detected which cover most of the genome, including large regions where genes have yet to be identified. Based on sequence comparisons with known tRNAs, only those for phe, trp, and tyr are encoded in Paramecium mt DNA.

Analysis of NADH dehydrogenase proteins, ATPase subunit 9, cytochrome b, and ribosomal protein L14 encoded in the mitochondrial DNA of Paramecium

The mitochondrial (mt) encoded ndh1, ndh3, ndh4, ndh5, rpl14, cyt b and atp9 gene products were identified by sequence comparisons with known proteins. Amino acid sequence comparisons between predicted Paramecium mt gene products and proteins in current databases were quantitated approximately by the means of similarity scores for pairs of aligned sequences. The comparisons show that the Paramecium gene products are very divergent from all others with the exception of those from a closely related ciliate, Tetrahymena. The similarity scores of comparisons between a Paramecium mt DNA encoded protein, cytochrome b for example, and the homologous protein from a group of organisms as diverse as other protozoans, vertebrates, fungi, plants, and prokaryotes were all about the same. The Paramecium gene products appear to be equally divergent from proteins representing a number of different kingdoms and organelles.

An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes

Based on DNA and amino acid comparisons with known genes and their products, a region of the Paramecium aurelia mitochondrial (mt) genome has been found to encode the following gene products: (1) photosystem II protein G (psbG); (2) a large open reading frame (ORF400) which is also found encoded in the chloroplast (cp) DNA of tobacco (as ORF393) and liverwort (as ORF392), and in the kinetoplast maxicircle DNA of Leishmania tarentolae (as ORFs 3 and 4); (3) ribosomal protein L2 (rpl2); (4) ribosomal protein S12 (rps12); (5) ribosomal protein S14 (rps14); and (6) NADH dehydrogenase subunit 2 (ndh2). All of these genes have been found in cp DNA, but the psbG gene has never been identified in a mt genome, and ribosomal protein genes have never been located in an animal or protozoan mitochondrion. The ndh2 gene has been found in both mitochondria and plastids. The Paramecium genes are among the most divergent of those sequenced to date. Two of the genes are encoded on the strand of DNA complementary to that encoding all other known Paramecium mt genes. No gene contains an identifiable intron. The rps12 and psbG genes are probably overlapping. It is not yet known whether these genes are transcribed or have functional gene products. The presence of these genes in the mt genome raises interesting questions concerning their evolutionary origin.

Nucleotide sequences and expression in Escherichia coli of the in-phase overlapping Pseudomonas aeruginosa plcR genes

The translation products of chromosomal DNAs of Pseudomonas aeruginosa encoding phospholipase C (heat-labile hemolysin) have been examined in T7 promoter plasmid vectors and expressed in Escherichia coli cells. A plasmid carrying a 4.7-kilobase (kb) DNA fragment was found to encode the 80-kilodalton (kDa) phospholipase C as well as two more proteins with an apparent molecular mass of 26 and 19 kDa. Expression directed by this DNA fragment with various deletions suggested that the coding region for the two smaller proteins was contained in a 1-kb DNA region. Moreover, the size of both proteins was reduced by the same amount by an internal BglII-BglII DNA deletion, suggesting that they were translated from overlapping genes. Similar results were obtained with another independently cloned 6.1-kb Pseudomonas DNA, which in addition coded for a 31-kDa protein of opposite orientation. The nucleotide sequence of the 1-kb region above revealed an open reading frame with a signal sequence typical of secretory proteins and a potential in-phase internal translation initiation site. Pulse-chase and localization studies in E. coli showed that the 26-kDa protein was a precursor of a secreted periplasmic 23-kDa protein (PlcR1) while the 19-kDa protein (PlcR2) was mostly cytoplasmic. These results indicate the expression of Pseudomonas in-phase overlapping genes in E. coli.

Nucleotide sequence and expression of a phosphate-regulated gene encoding a secreted hemolysin of Pseudomonas aeruginosa

A 3.3-kilobase-pair fragment of Pseudomonas aeruginosa DNA containing the phospholipase C (heat-labile hemolysin) gene was sequenced, and the location of the gene was determined. The gene product contains at its NH2 terminus a 38-amino acid sequence which structurally resembles the signal peptides of other secreted proteins but is unusually long and positively charged (6+). The location of the translation start codon was determined by constructing a series of plasmids in which the promoter of a transcription vector was ligated to Pseudomonas DNA containing deletions at the 5' end of the gene. The plasmids were used to transform Escherichia coli, and the resulting clones were assayed for hemolysin activity. In addition, sizes of truncated proteins produced by mutants with translation terminators introduced at specific sites were analyzed in E. coli maxicells. The gene is transcribed, starting just upstream of the hemolysin gene, as an mRNA of approximately 2,800 bases. Analysis of the nucleotide sequence, analysis of mutants in maxicells, and transcriptional studies indicate that the hemolysin is part of an operon composed of two genes. Phosphate regulation of the operon is at the transcriptional level. The location of the 5' end of the transcript was determined by S1 mapping.

Paramecium mitochondrial DNA sequences and RNA transcripts for cytochrome oxidase subunit I, URF1, and three ORFs adjacent to the replication origin

A 2-kb region adjacent to the replication origin (ori) and a 3-kb region located between the small and large ribosomal RNAs of Paramecium mitochondrial (mt) DNA have been sequenced and the locations of their transcripts determined. The ori segment contains four transcripts, some of which are overlapping, which encode a known protein and two other open reading frames. The other segment encodes, on separate transcripts, the cytochrome c oxidase subunit one gene (COI) and the URF1 gene (ND1) common to most mt genomes. All these genes have the same orientation and do not contain introns. The COI gene is the most divergent of those known and has an internal 108 amino acid 'insert' not found in COI genes from other organisms. With these data it is possible to define a probable Paramecium mt genetic code. With the exception that TGA codes for tryptophan and the use of different start codons, Paramecium mtDNA appears to follow the universal code. GTA possibly can be used as a start codon.

Identification of Paramecium mitochondrial proteins using antibodies raised against fused mitochondrial gene products

Paramecium aurelia mitochondrial (mt) DNA fragments carrying the coding regions for two proteins, P1 (in the region adjacent to the origin of replication) and COII (subunit II of cytochrome oxidase), were used to study mt gene expression. The sequence for the portion of mtDNA containing P1 has already been described [Pritchard et al., Gene 44 (1986) 243-253]. The complete nucleotide sequence of the portion containing the COII gene is presented here. An 18.5-kDa protein was produced in maxicells when a fragment containing a major portion of the sequence coding for P1 was used. This fragment and a fragment carrying the COII gene were cloned into the expression vector pTRPLE', and antibodies were raised against the resulting fusion proteins in an Escherichia coli lysate. Western blots of Paramecium mt extracts identified two proteins, one 21 kDa (COII) and the other 23.5 kDa (P1). The size of the P1 protein is in agreement with the size of the open reading frame in that region of mitochondrial DNA. Based on extensive amino acid homology to the Paramecium gene and limited homology to COII genes from other organisms, the COII gene in another ciliate, Tetrahymena pyriformis, was identified just upstream of the small subunit rDNA in previously published sequences (Schnare et al., 1986). The size of the COII gene and the homology with the COII gene from Tetrahymena suggest that ATC, ATT, GTG and GTC could be used as translational initiators in Paramecium mitochondria.

Inter-species sequence diversity in the replication initiation region of Paramecium mitochondrial DNA

Mitochondrial DNA from Paramecium aurelia is a linear molecule. Replication is initiated at a unique cross-linked molecular terminus. During replication dimer length molecules, consisting of two head-to-head monomers, are generated. We have cloned the head-to-head dimer initiation region from five different species and several stocks (or races) within species and determined its DNA sequence. For all species, this dimer initiation region consists of a central non-palindromic sequence containing almost exclusively A and T, arranged in an array of direct tandem repeats. In an intra-species comparison, the sequences of the repeat units are relatively homogeneous; inter-species comparisons, however, show diversity except for a conserved "Goldberg-Hogness box", T-A-T-A-A-A-T-A. The size of a repeat unit and the number of repeats within a molecule can vary over a wide range, even in an intra-species comparison. Because of these wide inter-species variations observed, it is likely that the function of this region imposes few constraints on the sequence other than its high A + T content and possibly a Goldberg-Hogness box. The array of direct tandem repeats may have arisen from unequal recombination or crossover within this region. Adjacent to the non-palindromic region is a transcribed sequence which is highly conserved for all species and presumably represents a gene coding region.

The utilization of protein and energy during lactation in the rat, with particular regard to the use of fat accumulated in pregnancy

1. The deposition of fat during pregnancy and its subsequent mobilization during lactation was studied in the rat. The utilization of protein during lactation was also investigated. 2. Fat accumulation was rapid and continuous from early pregnancy. Approximately one-third was deposited subcutaneously, the remainder being stored in central depots. 3. The volume of milk produced during lactation was varied by offering protein at two concentrations from day 2 post partum. Optimum lactation was achieved with a high-protein diet. The dams lost no body protein, but 60% of the total body fat was mobilized, despite a marked increase in food consumption. On a low-protein diet, food intake did not rise during lactation. Some body protein was catabolized and, again, 60% of the fat was mobilized although milk output, as judged by the gain in carcass energy of their pups, was reduced to approximately one-third of optimum. 4. Protein was used more efficiently by lactating rats, when compared with virgin controls. 5. We conclude that fat stored during pregnancy makes a major contribution to the energy costs of lactation, and that its mobilization is under hormonal rather than dietary control.

Replication of linear mitochondrial DNA from Paramecium: sequence and structure of the initiation-end crosslink

Replication of the 14-micrometer linear Paramecium mitochondrial DNA is initiated by a crosslinking of the duplex strands at the initiation end of the molecule. As a consequence of the crosslink, a head-to-head dimer molecule, or palindrome, is a replicative intermediate. The central region of the dimer molecules of two species was cloned and sequenced, In the distal regions, the sequence is palindromic as expected; however, in the central region, there is a nonpalindromic sequence that is rich in A + T and contains direct tandem repeats. It is proposed that the nonpalindromic sequence constitutes the crosslink. Implications for the replication scheme are discussed. The model is unlike any other for a linear DNA.

Cloning and characterization of Paramecium mitochondrial DNA replication initiation regions

Fragments containing the replication-initiation region of mitochondrial (mt) DNA from four species of Paramecium aurelia were ligated to the pBR322 plasmid and used to transform Escherichia coli. The criteria for identifying the desired mitochondrial DNA restriction fragments were based on the palindromic dimer structure of the replicative intermediate of this DNA. The nature of the cloned sequences was verified by hybridization to mitochondrial DNA fragments containing the initiation region, by determining the size of snapback renaturation products, and by determining the symmetry of restriction-endonuclease sites within the clones. Heterologous hybridization experiments showed that one species' initiation region is not homologous to the other three. Cleavage patterns of each of the clones by 18 different restriction enzymes were determined. There are no sites within approx. 250 bp of the center of the insert of any clone although there are numerous cleavages in more distal regions. These sites are generally symmetric about the center of the insert as expected for a palindromic structure. The characteristics of the cloned sequences support a proposed replication model for all four species studied.

Accessibility of some regions of DNA in chromatin (chicken erythrocytes) to single strand-specific nucleases

The susceptibility of the DNA in chromatin to single strand-specific nucleases was examined using nuclease P1, mung bean nuclease, and venom phosphodiesterase. A stage in the reaction exists where the size range of the solubilized products is similar for each of the three nucleases and is nearly independent of incubation time. During this stage, the chromatin fragments sediment in the range of 30 to 100 S and contain duplex DNA ranging from 1 to 10 million daltons. Starting with chromatin depleted of histones H1 and H5 similar fragments are generated. In both cases these nucleoprotein fragments are reduced to nucleosomes and their multimers by micrococcal nuclease. Thus, chromatin contains a limited number of DNA sites which are susceptible to single strand-specific nucleases. These sites occur at intervals of 8 to 80 nucleosomes and are distributed throughout the chromatin. Nucleosome monomers, dimers, or trimers were not observed at any stage of single strand-specific nuclease digestion of nuclei, H1- and H5-depleted chromatin, or micrococcal nuclease-generated oligonucleosomes. Each of the three nucleases converted mononucleosomes (approximately 160 base pairs) to nucleosome cores (approximately 140 base pairs) probably by exonucleolytic action that was facilitated by the prior removal of H1 and H5. The minichromosome of SV40 is highly resistant to digestion by nuclease P1.

Specific cleavages inflicted by venom phosphodiesterase on superhelical phiX174 DNA

A single strand specific endonuclease, venom phosphodiesterase, acting on superhelical phiX174 DNA, inflicts at least seven specific cleavages. Six of these were located to within approximately +/-40 base-pairs by mapping with restriction endonucleases. They are at 12%, 27.4%, 42.7%, 47.5%, 76.1%, and 82.5%. All of these sites lie within regions containing runs of 16 or more base-pairs, of which 12 or more are A and T. Other similarly (A + T)-rich regions in the genome are not cleaved by the enzyme. Increasing the superhelical density of the substrate did not alter the locations of the cleavage sites. There is no correlation between the locations of the cleavage sites and the three known major promoter sites. Only two of five postulated transcription termination sites are cleaved by phosphodiesterase even though all of these terminators contain (A + T)-rich regions. The area containing the origin of viral DNA replication, which includes an (A + T)-rich sequence, is not cleaved.

An endonuclease activity of venom phosphodiesterase specific for single-stranded and superhelical DNA

A homogeneous preparation of venom phosphodiesterase from Crotalus adamanteus possesses an intrinsic endonuclease activity, specific for superhelical (form I) and single-stranded DNA. The phosphodiesterase degrades single-stranded T7 DNA by endonucleolytic cleavages. Duplex T7 DNA is hydrolyzed by the liberation of acid-soluble products simultaneously from the 3' and 5' termini but without demonstrable internal scissions in duplex regions. Since venom phosphodiesterase is known to hydrolyze oligonucleotides stepwise from the 3' termini, the cleavage at the 5' end of duplex T7 DNA is ascribed to an endonuclease activity. Form I PM2 DNA is nicked to yield first relaxed circles and then linear DNA which is subsequently hydrolyzed only from the chain termini. The linear duplex DNA intermediates consist of a discrete series of fragments (11 are usually resolved on agarose gels) with initial molecular weights ranging from 6.3 x 10(6) (the intact PM2 DNA size) to approximately 1 x 10(6). The cleavage of the form I molecule must, therefore, occur at a limited number of unique sites. The enzyme also cleaves nonsuperhelical, covalently closed circular PM2 DNA but at a 10(4) times slower rate. Both the endonuclease activity on form I DNA and the known exonuclease activity co-migrate on polyacrtkanude gels, are optimally active at pH 9, are stimulated by small concentrations of Mg2+, and are similarly inactivated by heat, reducing agents, and EDTA.