Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

A genome resource for Acacia, Australia's largest plant genus

Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.

Phylogeny and classification of the Australasian and Indomalayan mimosoid legumes Archidendron and Archidendropsis (Leguminosae, subfamily Caesalpinioideae, mimosoid clade)

The morphologically variable genus Archidendron is the second largest mimosoid legume genus from the Indomalayan-Australasian region, yet it has not been well represented in phylogenetic studies. Phylogenies that have included multiple representatives of Archidendron suggest it may not be monophyletic, and the same applies to Archidendropsis, another understudied genus of the Archidendron clade. The most comprehensive phylogeny of Archidendron and Archidendropsis to date is presented, based on four nuclear markers (ITS, ETS, SHMT and RBPCO). Exemplars from all genera of the wider Archidendron clade are sampled, including representatives of all series within Archidendron and the two subgenera of Archidendropsis. Our results confirm that Archidendron and Archidendropsis are not monophyletic. Within Archidendron, only one series (ser. Ptenopae) is resolved as monophyletic and species of Archidendron are divided into two primarily geographic lineages. One clade is distributed in western Malesia and mainland Asia and includes most representatives of series Clypeariae, while the other is mostly restricted to eastern Malesia and Australia and includes representatives of the seven other series plus two samples of series Clypeariae. No taxonomic changes are made for Archidendron due to the high level of topological uncertainty and the lack of discrete macromorphological characters separating these two lineages. Each of the two subgenera of Archidendropsis is monophyletic but they are not closely related. A new genus endemic to Queensland (Australia), Heliodendron Gill.K. Br. & Bayly, gen. nov., is described for the former Archidendropsissubg.Basaltica, and combinations for its three species are proposed: Heliodendronbasalticum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., Heliodendronthozetianum (F. Muell.) Gill.K. Br. & Bayly, comb. nov., and Heliodendronxanthoxylon (C.T. White & W.D. Francis) Gill.K. Br. & Bayly, comb. nov.

Incidence of hyperaccumulation and tissue-level distribution of manganese, cobalt, and zinc in the genus Gossia (Myrtaceae)

The rare phenomenon of plant manganese (Mn) hyperaccumulation within the Australian flora has previously been detected in the field, which suggested that the tree genus Gossia (Myrtaceae) might contain new Mn hyperaccumulators. We conducted the first growth experiment on Gossia using a multi-factorial dosing trial to assess Mn, cobalt (Co), and zinc (Zn) (hyper)accumulation patterns in selected Gossia species (G. fragrantissima and G. punctata) after a systematic assessment of elemental profiles on all holdings of the genus Gossia at the Queensland Herbarium using handheld X-ray fluorescence spectroscopy. We then conducted detailed in situ analyses of the elemental distribution of Mn, Co, Zn and other elements at the macro (organ) and micro (cellular) levels with laboratory- and synchrotron-based X-ray fluorescence microscopy (XFM). Gossia pubiflora and Gossia hillii were newly discovered to be Mn hyperaccumulator plants. In the dosing trial, G. fragrantissima accumulated 17 400 µg g-1 Mn, 545 µg g-1 Co, and 13 000 µg g-1 Zn, without signs of toxicity. The laboratory-based XFM revealed distinct patterns of accumulation of Co, Mn, and Zn in G. fragrantissima, while the synchrotron XFM showed their localization in foliar epidermal cells, and in the cortex and phloem cells of roots. This study combined novel analytical approaches with controlled experimentation to examine metal hyperaccumulation in slow-growing tropical woody species, thereby enabling insight into the phenomenon not possible through field studies.

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

PREMISE

Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids.

METHODS

We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids.

RESULTS

Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well-supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids.

CONCLUSIONS

Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation.

Distribution and chemical form of selenium in Neptunia amplexicaulis from Central Queensland, Australia

Selenium (Se), a trace element essential for human and animal biological processes, is deficient in many agricultural soils. Some extremely rare plants can naturally accumulate extraordinarily high concentrations of Se. The native legume Neptunia amplexicaulis, endemic to a small area near Richmond and Hughenden in Central Queensland, Australia, is one of the strongest Se hyperaccumulators known on Earth, with foliar concentrations in excess of 4000 μg Se g^-1 previously recorded. Here, we report on the Se distribution at a whole plant level using laboratory micro X-ray Fluorescence Microscopy (μXRF) and scanning electron microscopy (SEM-EDS), as well as on chemical forms of Se in various tissues using liquid chromatography-mass spectrometry (LC-MS) and synchrotron X-ray absorption spectroscopy (XAS). The results show that Se occurs in the forms of methyl-selenocysteine and seleno-methionine in the foliar tissues, with up to 13 600 μg Se g^-1 total in young leaves. Selenium was found to accumulate primarily in the young leaves, flowers, pods and taproot, with lower concentrations present in the fine-roots and stem and the lowest present in the oldest leaves. Trichomes were not found to accumulate Se. We postulate that Se is (re)distributed in this plant via the phloem from older leaves to newer leaves, using the taproot as the main storage organ. High concentrations of Se in the nodes (pulvini) indicate this structure may play an important a role in Se (re)distribution. The overall pattern of Se distribution was similar in a non-Se tolerant closely related species (Neptunia gracilis), although the prevailing Se concentrations were substantially lower than in N. amplexicaulis.

The complete chloroplast genome sequence of Spyridium parvifolium var. parvifolium (family Rhamnaceae; tribe Pomaderreae)

We assembled the complete chloroplast genome of the Australian shrub Spyridium parvifolium var. parvifolium. The genome was 161,012 bp in length, with a pair of inverted repeats (IRs) of 26,515 bp, separated by a large single copy (LSC) region of 88,814 bp and a small single copy region (SCC) of 19,168 bp. The GC content was 36.9%. In total, 130 genes were annotated, including 86 protein coding genes, 36 tRNA genes and 8 rRNA genes. Phylogenetic analysis of 56 chloroplast genes placed this genome of S. parvifolium var. parvifolium within the family Rhamnaceae.

Evidence for induction of humoral and cytotoxic immune responses against devil facial tumor disease cells in Tasmanian devils (Sarcophilus harrisii) immunized with killed cell preparations

Tasmanian devils (Sarcophilus harrisii) risk extinction from a contagious cancer, devil facial tumour disease (DFTD) in which the infectious agent is the tumor cell itself. Because devils are unable to produce an immune response against the tumor cells no devil has survived 'infection'. To promote an immune response we immunized healthy devils with killed DFTD tumor cells in the presence of adjuvants. Immune responses, including cytotoxicity and antibody production, were detected in five of the six devils. The incorporation of adjuvants that act via toll like receptors may provide additional signals to break 'immunological ignorance'. One of these devils was protected against a challenge with viable DFTD cells. This was a short-term protection as re-challenge one year later resulted in tumor growth. These results suggest that Tasmanian devils can generate immune responses against DFTD cells. With further optimization of immune stimulation it should be possible to protect Tasmanian devils against DFTD with an injectable vaccine.

High phylogenetic diversity of the cat flea (Ctenocephalides felis) at two mitochondrial DNA markers

The cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) (Bouché), is the most common flea species found on cats and dogs worldwide. We investigated the genetic identity of the cosmopolitan subspecies C. felis felis and evaluated diversity of cat fleas from Australia, Fiji, Thailand and Seychelles using mtDNA sequences from cytochrome c oxidase subunit I (cox1) and II (cox2) genes. Both cox1 and cox2 confirmed the high phylogenetic diversity and paraphyletic origin of C. felis felis. The African subspecies C. felis strongylus (Jordan) is nested within the paraphyletic C. felis felis. The south East Asian subspecies C. felis orientis (Jordan) is monophyletic and is supported by morphology. We confirm that Australian cat fleas belong to C. felis felis and show that in Australia they form two distinct phylogenetic clades, one common with fleas from Fiji. Using a barcoding approach, we recognize two putative species within C. felis (C. felis and C. orientis). Nucleotide diversity was higher in cox1 but COX2 outperformed COX1 in amino acid diversity. COX2 amino acid sequences resolve all phylogenetic clades and provide an additional phylogenetic signal. Both cox1 and cox2 resolved identical phylogeny and are suitable for population structure studies of Ctenocephalides species.

Changes in problem-solving appraisal after cognitive therapy for the prevention of suicide

BACKGROUND

Cognitive therapy has been found to be effective in decreasing the recurrence of suicide attempts. A theoretical aim of cognitive therapy is to improve problem-solving skills so that suicide no longer remains the only available option. This study examined the differential rate of change in problem-solving appraisal following suicide attempts among individuals who participated in a randomized controlled trial for the prevention of suicide.

METHOD

Changes in problem-solving appraisal from pre- to 6-months post-treatment in individuals with a recent suicide attempt, randomized to either cognitive therapy (n = 60) or a control condition (n = 60), were assessed by using the Social Problem-Solving Inventory-Revised, Short Form.

RESULTS

Improvements in problem-solving appraisal were similarly observed for both groups within the 6-month follow-up. However, during this period, individuals assigned to the cognitive therapy condition demonstrated a significantly faster rate of improvement in negative problem orientation and impulsivity/carelessness. More specifically, individuals receiving cognitive therapy were significantly less likely to report a negative view toward life problems and impulsive/carelessness problem-solving style.

CONCLUSIONS

Cognitive therapy for the prevention of suicide provides rapid changes within 6 months on negative problem orientation and impulsivity/carelessness problem-solving style. Given that individuals are at the greatest risk for suicide within 6 months of their last suicide attempt, the current study demonstrates that a brief cognitive intervention produces a rapid rate of improvement in two important domains of problem-solving appraisal during this sensitive period.

Reversible infantile respiratory chain deficiency is a unique, genetically heterogenous mitochondrial disease

OBJECTIVES

Homoplasmic maternally inherited, m.14674T>C or m. 14674T>G mt-tRNA(Glu) mutations have recently been identified in reversible infantile cytochrome c oxidase deficiency (or 'benign COX deficiency'). This study sought other genetic defects that may give rise to similar presentations.

PATIENTS

Eight patients from seven families with clinicopathological features of infantile reversible cytochrome c oxidase deficiency were investigated.

METHODS

The study reviewed the diagnostic features and performed molecular genetic analyses of mitochondrial DNA and nuclear encoded candidate genes.

RESULTS

Patients presented with subacute onset of profound hypotonia, feeding difficulties and lactic acidosis within the first months of life. Although recovery was remarkable, a mild myopathy persisted into adulthood. Histopathological findings in muscle included increased lipid and/or glycogen content, ragged-red and COX negative fibres. Biochemical studies suggested more generalised abnormalities than pure COX deficiency. Clinical improvement was reflected by normalisation of lactic acidosis and histopathological abnormalities. The m.14674T>C mt-tRNA(Glu) mutation was identified in four families, but none had the m. 14674T>G mutation. Furthermore, in two families pathogenic mutations were also found in the nuclear TRMU gene which has not previously been associated with this phenotype. In one family, the genetic aetiology still remains unknown.

CONCLUSIONS

Benign COX deficiency is better described as 'reversible infantile respiratory chain deficiency'. It is genetically heterogeneous, and patients not carrying the m.14674T>C or T>G mt-tRNA(Glu) mutations may have mutations in the TRMU gene. Diagnosing this disorder at the molecular level is a significant advance for paediatric neurologists and intensive care paediatricians, enabling them to select children with an excellent prognosis for continuing respiratory support from those with severe mitochondrial presentation in infancy.

Two cases with progressive cystic leukoencephalopathy

Leukoencephalopathies with cystic changes in the white matter on magnetic resonance imaging are aetiologically heterogeneous neurological disorders seen in children. A group of leukoencephalopathies characterised by white matter lesions progressing to multifocal cystic degeneration has been reported in various disorders, including mitochondrial enzyme deficiencies, leukodystrophies, and infectious processes. We report two patients with leukoencephalopathy showing progressive cystic changes on serial MRI, and magnetic resonance spectroscopy resembling progressive cavitating leukoencephalopathy.

Mitochondrial cytopathies, phenotypic heterogeneity and a high incidence

Mitochondrial respiratory chain disorders account for significant and varied presentations in paediatric practice. The true prevalence of these disorders in the paediatric population is still not well documented with predicted geographic variation. We report a retrospective analysis over a seven year period of cases presenting to a tertiary care centre and associated clinical features. The overall prevalence of mitochondrial disorders in our population is higher than expected (1/9,000 births), explained in part by multiple presentations in a consanguineous subgroup of the population (Irish travellers).

Pyruvate dehydrogenase E3 binding protein (protein X) deficiency

Pyruvate dehydrogenase (PDH) deficiency is a major cause of neurological dysfunction and lactic acidosis in infancy and early childhood. The great majority of cases (>80%) result from mutations in the X-linked gene for the E1alpha subunit of the complex (PDHA1). Mutations in the genes for the other subunits have all been described, but only dihydrolipoamide dehydrogenase (E3) and E3 binding protein (E3BP) defects contribute significantly to the total number of patients with PDH deficiency. Although previously considered rare, with only 13 reported cases, we have found that mutations in PDX1, the gene for the E3 binding protein, are in fact relatively common. Clinical, biochemical, and genetic features of six new patients (four males, two females; age range 15mo-6y) with mutations in this gene are compared with previously reported cases. All patients with E3BP deficiency identified to date have mutations which completely prevent synthesis of the protein product. However, they are generally less severely affected than patients with PDHA1 mutations, although there is considerable overlap in clinical and neuroradiological features.

Detection of Anaplasma platys and Babesia canis vogeli and their impact on platelet numbers in free-roaming dogs associated with remote Aboriginal communities in Australia

OBJECTIVE

To detect Anaplasma platys and Babesia canis vogeli infection, using polymerase chain reaction (PCR)-based assays, in free-roaming dogs associated with eight Aboriginal communities in remote areas of Australia and to determine the impact of infection through the assessment of platelet numbers.

PROCEDURES

Blood samples from 215 dogs were screened by PCR for A platys and B canis vogeli using established genus-specific DNA primers for the 16S and 18S rRNA genes respectively. Both A platys DNA and B canis vogeli DNA were confirmed from the screening PCR either by sequencing or by the use of species-specific primers. Peripheral blood films from 92 of the 215 dogs were used to estimate platelet numbers through an indirect method.

RESULTS

Of 215 dogs, 69 (32%) were positive for A platys, 22 (10%) for B canis vogeli and 24 (11%) for both. The two organisms were detected singularly and as coinfection in all communities. For the 92 dogs in which peripheral blood films were examined, the mean estimated platelet counts for the non-infected dogs was 318 x 10(9)/L, those infected with A platys alone was 256 x 10(9)/L, those with B canis vogeli alone was 276 x 10(9)/L and those infected with both parasites was 169 x 10(9)/L. In young dogs, infection produced significantly decreased mean platelet counts when compared to uninfected dogs. Thrombocytopenia (< 200 x 10(9)/L) was detected in 18 (51%) dogs infected with A platys alone, 3 (33%) dogs infected with B canis vogeli alone, 13 (72%) dogs coinfected, and 8 (27%) uninfected dogs.

CONCLUSIONS

A platys and B canis vogeli infection, either singularly or together, was widespread in free roaming dogs associated with remote Aboriginal communities in the Northern Territory and north-western New South Wales. Moreover, both A platys and B canis vogeli infections were associated with a reduction in mean platelet numbers in dog populations, particularly in young dogs. The fact that 51% of dogs infected with A platys alone and 72% dogs coinfected were thrombocytopenic compared to 27% of uninfected dogs suggests that the organism alone or in combination with B canis vogeli has the potential to cause thrombocytopenia and perhaps contribute to a clinical bleeding disorder in infected dogs.

Congenital brain malformations in mitochondrial disease

The majority of patients with mitochondrial disease have some degree of neuropathology and this is usually degenerative in nature. However, in a subset of mitochondrial diseases there are additional specific and characteristic congenital malformations in the brain. These developmental abnormalities are not unique to mitochondrial diseases and their association with only some conditions suggests that they are not simply due to energy deprivation or accumulation of metabolites such as lactic acid. Pathogenic mechanisms are at present unknown, but interference with neurotransmitter homeostasis, in addition to altered energy metabolism, may be important. The postnatal evolution of the neuropathology in these conditions and the type and pattern of the malformations suggest secondary degeneration of specific brain structures during fetal life rather than primary interference with developmental pathways.

Pyruvate dehydrogenase deficiency presenting as dystonia in childhood

Two individuals with pyruvate dehydrogenase (PDH) deficiency due to missense mutations in the gene for the E1alpha subunit (PDHA1) presented during childhood with dystonia. The first patient, a male, presented at age 4 years with dystonia affecting the lower limbs, which responded to treatment with combined carbidopa and levodopa. The second patient, a female, was first investigated at age 6 years because of a dystonic gait disorder. In both patients, the main clue to the biochemical diagnosis was a raised concentration of lactate in the cerebrospinal fluid. PDH activity was significantly reduced in cultured fibroblasts in both cases. Dystonia is a previously unrecognized major manifestation of PDH deficiency and is of particular interest as the mutations in the PDHA1 gene in these patients have both been identified previously in individuals with typical presentations of the condition.

Marked increases in psychopathology found in a 30-year cohort comparison of suicide attempters

BACKGROUND

Although several epidemiological studies have found increases in the percentages of people who have made a suicide attempt, few cohort comparisons have been conducted to determine changes within this population over time. The purpose of this investigation was to determine if there have been changes in the clinical profile of suicide attempters in recent decades.

METHOD

Comparisons between a sample of 258 suicide attempters evaluated between 1970 and 1973 and a second sample of 179 suicide attempters evaluated between 1999 and 2002 were made on depression, hopelessness, suicide intent, drug use, history of suicide attempts and subsequent suicide attempts.

RESULTS

Present-day suicide attempters were found to exhibit greater levels of depression (p = 0.031), hopelessness (p = 0.008), suicide intent (p < 0.001), and had much higher rates of illicit drug use (p < 0.001). Almost twice as many of the present-day suicide attempters had histories of four or more suicide attempts (p < 0.001), and the present-day suicide attempters made subsequent suicide attempts at close to four times the rate in the year following the index attempt (p < 0.001).

CONCLUSIONS

The present-day suicide attempters exhibited greater levels of psychopathology on every major variable assessed. Replication is necessary and public health implications are discussed.

A pathogenic glutamate-to-aspartate substitution (D296E) in the pyruvate dehydrogenase E1 subunit gene PDHA1

In a patient with fatal neonatal lactic acidosis due to pyruvate dehydrogenase deficiency, the only potential mutation detected was c.888C>G in PDHA1, the gene for the E1alpha subunit of the complex. This would result in a substitution of glutamate for aspartate (D296E). Pathogenicity of this minor alteration in amino acid sequence was demonstrated by expression studies. By comparing the mutant sequence with the known structures of the E1 components of pyruvate dehydrogenase and the closely related branched chain alpha-ketoacid dehydrogenase, an explanation for the profound consequences of the mutation can be proposed.

Diagnostic difficulties with common SURF1 mutations in patients with cytochrome oxidase-deficient Leigh syndrome

In three unrelated patients with systemic cytochrome oxidase deficiency resulting from mutations in the SURF1 gene, the same mutation in the splice donor site of intron 3 was identified. All three patients were compound heterozygotes, two for the common insertion/deletion mutation in exon 4. In all three cases, complete definition of the causative mutations was only resolved by combined analysis of cDNA and genomic DNA. Several factors were identified that contributed to the diagnostic difficulties: preferential amplification of deleted cDNA, significant formation of heteroduplexes in cDNA PCR amplification and unequal representation of heterozygous peaks in genomic DNA sequences. These patients emphasize the need to perform mutation analysis on both cDNA and genomic DNA wherever possible.

Lactic acidosis and developmental delay due to deficiency of E3 binding protein (protein X) of the pyruvate dehydrogenase complex

Pyruvate dehydrogenase deficiency is an important cause of primary lactic acidosis. Most cases occur as a result of mutations in the gene for the E1 alpha subunit of the complex, with a small number resulting from mutations in genes for other components, most commonly the E3 and E3-binding protein subunits. We describe pyruvate dehydrogenase E3-binding protein deficiency in two siblings in each of two unrelated families from Kuwait. The index patient in each family had reduced pyruvate dehydrogenase activity in cultured fibroblasts and no detectable immunoreactive E3-binding protein. Both were homozygous for nonsense mutations in the E3-binding protein gene, one involving the codon for glutamine 266, the other the codon for tryptophan 5.

Dysfunctional beliefs discriminate personality disorders

This study examines whether specific sets of dysfunctional beliefs are differentially associated with five personality disorders (PDs) as predicted by cognitive theory. Seven hundred fifty-six psychiatric outpatients completed the Personality Belief Questionnaire (PBQ) at intake and were assessed for PDs using a standardized clinical interview conducted by assessors who were blind to patients' PBQ responses. Findings showed that patients with avoidant, dependent, obsessive-compulsive, narcissistic, and paranoid PDs preferentially endorsed PBQ beliefs theoretically linked to their specific disorders. The study results support the cognitive theory of personality disorders. Suggestions are made regarding the clinical utility of the PBQ with personality-disordered patients and future research on the PBQ.

Response to cognitive therapy in depression: the role of maladaptive beliefs and personality disorders

This study examined whether personality disorder status and beliefs that characterize personality disorders affect response to cognitive therapy. In a naturalistic study, 162 depressed outpatients with and without a personality disorder were followed over the course of cognitive therapy. As would be hypothesized by cognitive theory (A. T. Beck & A. Freeman, 1990), it was not personality disorder status but rather maladaptive avoidant and paranoid beliefs that predicted variance in outcome. However, pre- to posttherapy comparisons suggested that although patients with or without comorbidity respond comparably to "real-world" cognitive therapy, they report more severe depressive symptomatology at intake and more residual symptoms at termination.

Detection of Ehrlichia platys in dogs in Australia

OBJECTIVE

To describe the detection of Ehrlichia platys in free-roaming dogs in Central Australia.

PROCEDURE

Blood samples were collected from four dogs and examined for bacterial 16S ribosomal DNA using Polymerase Chain Reaction (PCR)-based assays. The three positive samples obtained were then sequenced and identification of the PCR product carried out. As a result of all three samples being identical to or closely related to part of the 16S rRNA gene of E. platys, blood samples were subsequently obtained from a further 24 dogs. These samples were screened using a PCR-assay to determine the presence of Ehrlichia DNA using genus-specific primers. The positive samples obtained from the screening process were then subjected to a further PCR-assay using E. platys specific primers.

RESULTS

Of 28 dogs sampled, Ehrlichia DNA was detected in the blood of 13 dogs. Sequencing of the amplicons obtained indicated a high homology with the 16S rRNA gene for E. platys. When the E. platys-specific PCR was performed for 10 of those dogs, the 678 bp product obtained from the PCR amplification confirmed the identification as part of the 16S rRNA gene of E. platys in all 10 dogs.

CONCLUSION

This study reports for the first time Ehrlichia carriage by dogs in Australia. It also indicates the usefulness of the PCR technique in rapidly and accurately identifying diseases that are otherwise difficult to detect. By using universal primers directed against bacterial 16S ribosomal DNA and sequencing analysis, the detection of potentially pathogenic Ehrlichia organisms that had not previously been found in Australia has been made possible.

Mean Beck Depression Inventory-II scores by severity of major depressive episode

The Beck Depression Inventory-II total scores of 35 (14%) outpatients who were diagnosed with a mild DSM-IV Major Depressive Episode (MDE), 144 (55%) outpatients with a moderate MDE, and 81 (31%) outpatients with a severe MDE were compared. The mean BDI-II total scores were, respectively, 18 (SD = 8, 99% CI 12-23), 27 (SD = 10, 99% CI 24-29), and 34 (SD = 10, 99% CI 30-37) (F2.257 = 33.25, p<.001). The mean BDI-II total score of the outpatients with a severe specifier was significantly higher than the mean BDI-II total score of the outpatients with a moderate specifier which was, in turn, significantly higher than the mean BDI-II total score of the outpatients with a mild specifier.

A SURF1 gene mutation presenting as isolated leukodystrophy

Mitochondrial respiratory chain defects are increasingly recognized in patients with leukodystrophy. We report the first case of leukodystrophy with systemic cytochrome oxidase deficiency caused by a loss of function mutation in the SURF1 gene in a 2-year-old girl presenting with failure to thrive, global neurodevelopmental regression, and lactic acidosis. Although all previously reported mutations in the SURF1 gene have been found in patients with cytochrome oxidase (COX)-deficient Leigh syndrome, the phenotype associated with SURF1 protein deficiency should be extended to include leukodystrophy.

Response to cognitive therapy in depression: the role of maladaptive beliefs and personality disorders

This study examined whether personality disorder status and beliefs that characterize personality disorders affect response to cognitive therapy. In a naturalistic study, 162 depressed outpatients with and without a personality disorder were followed over the course of cognitive therapy. As would be hypothesized by cognitive theory (A. T. Beck & A. Freeman, 1990), it was not personality disorder status but rather maladaptive avoidant and paranoid beliefs that predicted variance in outcome. However, pre- to posttherapy comparisons suggested that although patients with or without comorbidity respond comparably to "real-world" cognitive therapy, they report more severe depressive symptomatology at intake and more residual symptoms at termination.

The National Institutes of Health Clinical Center Digital Imaging Network, Picture Archival and Communication System, and Radiology Information System

In this work, we describe the digital imaging network (DIN), picture archival and communication system (PACS), and radiology information system (RIS) currently being implemented at the Clinical Center, National Institutes of Health (NIH). These systems are presently in clinical operation. The DIN is a redundant meshed network designed to address gigabit density and expected high bandwidth requirements for image transfer and server aggregation. The PACS projected workload is 5.0 TB of new imaging data per year. Its architecture consists of a central, high-throughput Digital Imaging and Communications in Medicine (DICOM) data repository and distributed redundant array of inexpensive disks (RAID) servers employing fiber-channel technology for immediate delivery of imaging data. On demand distribution of images and reports to clinicians and researchers is accomplished via a clustered web server. The RIS follows a client-server model and provides tools to order exams, schedule resources, retrieve and review results, and generate management reports. The RIS-hospital information system (HIS) interfaces include admissions, discharges, and transfers (ATDs)/demographics, orders, appointment notifications, doctors update, and results.

High-risk management guidelines for elderly suicidal patients in primary care settings

Older adults, especially older white men, are more likely to commit suicide than other age-groups. The assessment and management of suicide ideation and behavior for the elderly is especially relevant for primary care physicians because many patients visit their physician shortly before committing suicide. In 1993, the Agency for Health Care Policy and Research (AHCPR) released clinical practice guidelines for the treatment of depression in primary care settings. The AHCPR guidelines offered some assistance with respect to detecting and treating patients who are suicidal. However, these guidelines lacked detailed and specific instructions for managing high-risk patients within the context of intervention research. The current set of guidelines builds upon this previous work by describing (1) a general approach for interacting with suicidal patients; (2) structured assessments for determining the degree of risk for suicide; (3) crisis intervention strategies; and (4) ongoing management procedures for working with suicidal patients in primary care settings.

Sequence variations in the NDUFA1 gene encoding a subunit of complex I of the respiratory chain

NDUFA1 is one of the 36 nuclear genes encoding subunits of the mitochondrial complex I involved in the respiratory chain. The human NDUFA1 has been cloned, completely sequenced and mapped to Xq24. In the present study, we searched for sequence variations in NDUFA1 as causative defects in complex I deficiency using genomic DNA of 152 patients with various clinical phenotypes. The patient sample consisted of 54 patients (46 male and 8 female) with Leber heriditary optic neuropathy (LHON) from 48 unrelated families from Germany and 98 patients (72 male and 26 female) with biochemically proven complex I deficiency including Leigh syndrome. Patient DNA was used to amplify all three exons, including the exon/intron boundaries and the promoter region of NDUFA1 for heteroduplex analysis and direct sequencing. In the 152 patients tested, no mutation was found that could be related to any of the disease phenotypes included. However, three single-nucleotide polymorphisms (SNPs) located in the promoter region (SNP G/C at nt -71 and SNP T/C at nt -189) and in intron 1 (SNP T/G nt 1454) were discovered. Allele frequencies of the SNPs were estimated in a German and Estonian control population and compared to complex I-deficient patients. There was no significant difference between the control population, the LHON patients, or the severely affected patients with complex I deficiency, excluding an association of the polymorphisms with the diseases. Our results suggest that mutations in NDUFA1 do not cause the gender difference observed in clinically severe and complex phenotypes with complex I deficiency.

Synthesis of mitochondrial DNA in permeabilised human cultured cells

The mechanisms that underlie the maintenance of and increase in mutant mitochondrial DNA (mtDNA) are central to our understanding of mitochondrial disease. We have therefore developed a technique based on saponin permeabilisation that allows the study of mtDNA synthesis in intact cells. Permeabilisation of cells has been extensively used in an established method both for studying transcription and DNA replication in the nucleus and for measuring respiratory chain activities in mitochondria. We have quantitatively studied incorporation of radiolabelled DNA precursors into mtDNA in human cell lines derived from controls and from patients with mitochondrial DNA disease. Total cell DNA is extracted, restriction digested and Southern blotted, newly synthesised mtDNA being proportional to the label incorporated in each restriction band. A rate of synthesis can then be derived by estimating the relative steady-state mtDNA after probing with full-length mtDNA. Where co-existing mutant and wild-type mtDNA (heteroplasmy) can be distinguished using restriction digestion, their rates of synthesis can be compared within a single cell line. This will be particularly useful in elucidating the pathophysiology of mtDNA diseases in which the distribution of mutant and wild-type mtDNA in cell lines in patient tissues may evolve with time.

Psychometric properties of the Beck Self-Esteem Scales

The psychometric characteristics of the Beck Self-Esteem Scales (BSE) are described for 360 psychiatric outpatients. Patients rated their evaluative beliefs about themselves (Self Scale) and their beliefs about how others evaluate them (Other Scale). Both measures consist of 18 pairs of adjectives, e.g., lovable-unlovable, that are rated using a 10-point scale. The coefficient alphas for the Self Scale (0.94) and the Other Scale (0.95) indicated high internal consistency. Both scales were positively associated with other measures of self-esteem and negatively associated with measures of anxiety and depression. As predicted by the cognitive theory of depression, patients with a principal mood disorder scored significantly lower on the BSE than patients with a principal anxiety disorder. In addition, the mean scores for patients with major depression and dysthymia on the Self Scale were significantly lower than the mean scores for the Other Scale.

Suicide prevention in late life: directions for science and practice

Suicide among the elderly is a critical public health problem, yet there remains limited information on risk factors to target due to the few number of controlled studies that could help isolate and focus on the most potent risk factors. We suggest that because there are no proven, effective interventions showing reduced suicidal behaviors in older adults, the best current approach is to improve detection and treatment of later-life depression. This effort may be especially effective in primary care settings, where the majority of our nation's elderly seek and receive their mental health care. We review approaches to assessment and treatment of later life depression that seem most relevant for later life suicide prevention. Testing and determining whether these treatment approaches are effective is an immediate goal on the path to advancing the science and practice of late-life suicide prevention.

Risk factors for suicide in psychiatric outpatients: a 20-year prospective study

To determine the risk factors for suicide, 6,891 psychiatric outpatients were evaluated in a prospective study. Subsequent deaths for the sample were identified through the National Death Index. Forty-nine (1%) suicides were determined from death certificates obtained from state vital statistics offices. Specific psychological variables that could be modified by clinical intervention were measured using standardized scales. Univariate survival analyses revealed that the severity of depression, hopelessness, and suicide ideation were significant risk factors for eventual suicide. A multivariate survival analysis indicated that several modifiable variables were significant and unique risk factors for suicide, including suicide ideation, major depressive disorder, bipolar disorder, and unemployment status.

Arginine 302 mutations in the pyruvate dehydrogenase E1alpha subunit gene: identification of further patients and in vitro demonstration of pathogenicity

Three further patients with mutations in the codon for arginine 302 of the E1alpha subunit of the pyruvate dehydrogenase complex have been identified. Mutations in this codon have now been found in nine patients with pyruvate dehydrogenase deficiency in seven unrelated families, in sharp contrast to the great majority of other PDH E1alpha mutations which have been described in single individuals only. Because of the relatively high frequency of this mutation and because very few PDH E1alpha mutations have been demonstrated to be causative, we have established a system for analysing the consequences of defined mutations using transfection of normal and mutant PDH E1alpha cDNA into transformed human fibroblasts which have no endogenous E1alpha mRNA or protein. Using this test system, we have demonstrated that the R302C mutation results in the production of PDH E1alpha protein which is devoid of enzymic activity.

Mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1) in patients with a pyruvate dehydrogenase complex deficiency

Defects in the pyruvate dehydrogenase (PDH) complex are an important cause of primary lactic acidosis, a frequent manifestation of metabolic disease in children. Clinical symptoms can vary considerably in patients with PDH complex deficiencies, and almost equal numbers of affected males and females have been identified, suggesting an autosomal recessive mode of inheritance of the disease. However, the great majority of PDH complex deficiencies result from mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1). The major factors that contribute to the clinical variation in E1alpha deficiency and its resemblance to a recessive disease are developmental lethality in some males with severe mutations and the pattern of X-inactivation in females. To date, 37 different missense/nonsense and 39 different insertion/deletion mutations have been identified in the E1alpha subunit gene of 130 patients (61 females and 69 males) from 123 unrelated families. Insertion/deletion mutations occur preferentially in exons 10 and 11, while missense/nonsense mutations are found in all exons. In males, the majority of missense/nonsense mutations are found in exons 3, 7, 8 and 11, and three recurrent mutations at codons R72, R263 and R378 account for half of these patients with missense/nonsense mutations (25 of 50). A significantly lower number of females is found with missense/nonsense mutations (25). However, 36 females out of 55 affected patients have insertion/deletion mutations. The total number of female and male patients is thus almost the same, although a difference in the distribution of the type of mutations is evident between both sexes. In many families, the parents of the affected patients were studied for the presence of the PDHA1 mutation. The mutation was never present in the somatic cells of the father; in 63 mothers studied, 16 were carriers (25%). In four families, the origin of the new mutation was determined to be twice paternal and twice maternal.

Glucose transporters: structure, function and consequences of deficiency

There are two mechanisms for glucose transport across cell membranes. In the intestine and renal proximal tubule, glucose is transported against a concentration gradient by a secondary active transport mechanism in which glucose is cotransported with sodium ions. In all other cells, glucose transport is mediated by one or more of the members of the closely related GLUT family of glucose transporters. The pattern of expression of the GLUT transporters in different tissues is related to the different roles of glucose metabolism in different tissues. Primary defects in glucose transport all appear to be extremely rare and not all possible deficiencies have been identified. Deficiency of the secondary active sodium/glucose transporters result in glucose/galactose malabsorption or congenital renal glycosuria. GLUT1 deficiency produces a seizure disorder with low glucose concentration in cerebrospinal fluid and GLUT2 deficiency is the basis of the Fanconi-Bickel syndrome, which resembles type I glycogen storage disease.

Dichloroacetate stabilizes the mutant E1alpha subunit in pyruvate dehydrogenase deficiency

OBJECTIVE

To determine whether dichloroacetate (DCA) treatment can increase pyruvate dehydrogenase (PDH) activity in PDH-deficient cell lines harboring pathogenic mutations in the PDH E1alpha gene.

BACKGROUND

PDH deficiency is a nuclear-encoded mitochondrial disorder and a major recognized cause of neonatal encephalomyopathies associated with primary lactic acidosis. Over the last decade, DCA has been used therapeutically, but it has not been clear which patients might benefit. Recent studies suggest that chronic DCA treatment may act by increasing the stability of mutant E1alpha polypeptide. The relative effects of DCA treatment on PDH-deficient cell lines with E1alpha mutations primarily affecting polypeptide stability or catalytic activity were determined and the mechanism of enhancement of residual PDH activity explored.

METHODS

The effect of chronic 5-day DCA treatment on PDH activity was assessed in PDH-deficient cell lines containing the R378H, R141Q, K387(FS), and R302C E1alpha mutations. PDH subunit turnover and steady-state E1alpha levels before and after DCA treatment were measured in the R378H mutant line.

RESULTS

Chronic DCA treatment resulted in 25% (p = 0.0434), 31% (p = 0.0014) increases in PDH activity in the K387(FS) and R378H cell lines, both of which are associated with decreased mutant polypeptide stability. In the R378H mutant cell line, chronic DCA treatment increased steady-state E1alpha levels and slowed the rate of E1alpha turnover twofold. In contrast, PDH activity did not change in the chronically DCA-treated R302C mutant line, in which the mutant polypeptide has normal stability and reduced catalytic activity.

CONCLUSIONS

Chronic DCA treatment can increase PDH activity in PDH-deficient cell lines harboring mutations that affect E1alpha stability, suggesting a biochemical criterion by which DCA-responsive patients might be selected.

Suicide ideation at its worst point: a predictor of eventual suicide in psychiatric outpatients

Scales for measuring current suicide ideation (SSI-C), suicide ideation at its worst point in the patient's life (SSI-W), and hopelessness (BHS) were administered to 3,701 outpatients seeking psychiatric treatment. Thirty patients from this sample eventually committed suicide, within a mean of 4 years from the initial assessment. Based on cut-off scores derived from receiver operating characteristic (ROC) analyses, the SSI-W had an odds ratio of 13.84 for predicting suicide, whereas the SSI-C and the BHS had odds ratios of 5.42 and 6.43, respectively. The assessment of suicide ideation at its worst point identifies a subgroup of patients at relatively high risk for eventual suicide. Robust interventions and periodic monitoring for suicide ideation and hopelessness are recommended to reduce long-term suicide risk.

SURF1, encoding a factor involved in the biogenesis of cytochrome c oxidase, is mutated in Leigh syndrome

Leigh Syndrome (LS) is a severe neurological disorder characterized by bilaterally symmetrical necrotic lesions in subcortical brain regions that is commonly associated with systemic cytochrome c oxidase (COX) deficiency. COX deficiency is an autosomal recessive trait and most patients belong to a single genetic complementation group. DNA sequence analysis of the genes encoding the structural subunits of the COX complex has failed to identify a pathogenic mutation. Using microcell-mediated chromosome transfer, we mapped the gene defect in this disorder to chromosome 9q34 by complementation of the respiratory chain deficiency in patient fibroblasts. Analysis of a candidate gene (SURF1) of unknown function revealed several mutations, all of which predict a truncated protein. These data suggest a role for SURF1 in the biogenesis of the COX complex and define a new class of gene defects causing human neurodegenerative disease.

Inadequate response to therapy as a predictor of suicide

The role of response to cognitive therapy as a predictor of suicide was investigated by comparing 17 outpatients with mood disorders who committed suicide with 17 matched patients who did not commit suicide. The suiciders attended significantly fewer sessions of cognitive therapy and dropped out of therapy more frequently: 88% of the suiciders, compared to 53% of the controls, were rated by their therapists as requiring more treatment at termination. They also had higher levels of hopelessness at the termination of therapy. The results suggest that premature termination of therapy and inadequate response to treatment have unfavorable prognostic significance for eventual suicide.