Distinct SIV-specific CD8+ T cells in the lymph node exhibit simultaneous effector and stem-like profiles and are associated with limited SIV persistence.

Human immunodeficiency virus (HIV) cure efforts are increasingly focused on harnessing CD8+ T cell functions, which requires a deeper understanding of CD8+ T cells promoting HIV control. Here we identifiy an antigen-responsive TOXhiTCF1+CD39+CD8+ T cell population with high expression of inhibitory receptors and low expression of canonical cytolytic molecules. Transcriptional analysis of simian immunodeficiency virus (SIV)-specific CD8+ T cells and proteomic analysis of purified CD8+ T cell subsets identified TOXhiTCF1+CD39+CD8+ T cells as intermediate effectors that retained stem-like features with a lineage relationship with terminal effector T cells. TOXhiTCF1+CD39+CD8+ T cells were found at higher frequency than TCF1-CD39+CD8+ T cells in follicular microenvironments and were preferentially located in proximity of SIV-RNA+ cells. Their frequency was associated with reduced plasma viremia and lower SIV reservoir size. Highly similar TOXhiTCF1+CD39+CD8+ T cells were detected in lymph nodes from antiretroviral therapy-naive and antiretroviral therapy-suppressed people living with HIV, suggesting this population of CD8+ T cells contributes to limiting SIV and HIV persistence.

Activating and repressing gene expression between chromosomes during stochastic fate specification.

DNA elements act across long genomic distances to regulate gene expression. During transvection in Drosophila, DNA elements on one allele of a gene act between chromosomes to regulate expression of the other allele. Little is known about the biological roles and developmental regulation of transvection. Here, we study the stochastic expression of spineless (ss) in photoreceptors in the fly eye to understand transvection. We determine a biological role for transvection in regulating expression of naturally occurring ss alleles. We identify DNA elements required for activating and repressing transvection. Different enhancers participate in transvection at different times during development to promote gene expression and specify cell fates. Bringing a silencer element on a heterologous chromosome into proximity with the ss locus "reconstitutes" the gene, leading to repression. Our studies show that transvection regulates gene expression via distinct DNA elements at specific timepoints in development, with implications for genome organization and architecture.

Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies.

Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). We investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. The ss locus is in a compact state in undifferentiated cells. An early enhancer drives transcription in all R7 precursors, and the locus opens. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact, and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives large-scale decompaction and then compaction represses transcription, controls stochastic fate specification.

Interdependent regulation of stereotyped and stochastic photoreceptor fates in the fly eye.

Diversification of neuronal subtypes often requires stochastic gene regulatory mechanisms. How stochastically expressed transcription factors interact with other regulators in gene networks to specify cell fates is poorly understood. The random mosaic of color-detecting R7 photoreceptor subtypes in Drosophila is controlled by the stochastic on/off expression of the transcription factor Spineless (Ss). In SsON R7s, Ss induces expression of Rhodopsin 4 (Rh4), whereas in SsOFF R7s, the absence of Ss allows expression of Rhodopsin 3 (Rh3). Here, we find that the transcription factor Runt, which is initially expressed in all R7s, is sufficient to promote stochastic Ss expression. Later, as R7s develop, Ss negatively feeds back onto Runt to prevent repression of Rh4 and ensure proper fate specification. Together, stereotyped and stochastic regulatory inputs are integrated into feedforward and feedback mechanisms to control cell fate.

Asymmetric histone inheritance via strand-specific incorporation and biased replication fork movement.

Many stem cells undergo asymmetric division to produce a self-renewing stem cell and a differentiating daughter cell. Here we show that, similarly to H3, histone H4 is inherited asymmetrically in Drosophila melanogaster male germline stem cells undergoing asymmetric division. In contrast, both H2A and H2B are inherited symmetrically. By combining super-resolution microscopy and chromatin fiber analyses with proximity ligation assays on intact nuclei, we find that old H3 is preferentially incorporated by the leading strand, whereas newly synthesized H3 is enriched on the lagging strand. Using a sequential nucleoside analog incorporation assay, we detect a high incidence of unidirectional replication fork movement in testes-derived chromatin and DNA fibers. Biased fork movement coupled with a strand preference in histone incorporation would explain how asymmetric old and new H3 and H4 are established during replication. These results suggest a role for DNA replication in patterning epigenetic information in asymmetrically dividing cells in multicellular organisms.

Buffering and Amplifying Transcriptional Noise During Cell Fate Specification.

The molecular processes that drive gene transcription are inherently noisy. This noise often manifests in the form of transcriptional bursts, producing fluctuations in gene activity over time. During cell fate specification, this noise is often buffered to ensure reproducible developmental outcomes. However, sometimes noise is utilized as a "bet-hedging" mechanism to diversify functional roles across a population of cells. Studies of bacteria, yeast, and cultured cells have provided insights into the nature and roles of noise in transcription, yet we are only beginning to understand the mechanisms by which noise influences the development of multicellular organisms. Here we discuss the sources of transcriptional noise and the mechanisms that either buffer noise to drive reproducible fate choices or amplify noise to randomly specify fates.

On matters of mind and body: regarding Descartes.

In this paper the author considers Descartes' place in current thinking about the mind-body dilemma. The premise here is that in the history of ideas, the questions posed can be as significant as the answers acquired. Descartes' paramount question was 'How do we determine certainty?' and his pursuit of an answer led to cogito ergo sum. His discovery simultaneously raised the question whether mind is separate from or unified with the body. Some who currently hold that brain and subjectivity are unified contend that the philosopher 'split' mind from body and refer to 'Descartes' error'. This paper puts forward that Descartes' detractors fail to recognise Descartes' contribution to Western thought, which was to introduce the Enlightenment and to give a place to human subjectivity. Added to this, evidence from Descartes' correspondence with Princess Elisabeth of Bohemia supports the conclusion that Descartes did in fact believe in the unity of mind and body although he could not reconcile this rationally with the certainty from personal experience that they were separate substances. In this Descartes was engaged in just the same dilemma as that of current thinkers and researchers, a conflict which still is yet to be resolved.

Michael Fordham and the Journal of Analytical Psychology: the view from Hangman's Hill.

This short paper was presented to a conference in honour of the 60(th) year of the JAP and was one of others that acknowledged the contribution of Michael Fordham. The subtitle refers to the paper's overview of Fordham's published oeuvre and the particular place of the Journal of Analytical Psychology, for which he was the founding editor. Fordham's contribution to a Jungian-based model of development is discussed, with reference to his papers in the British Journal of Medical Psychology. The paper notes miscellaneous pieces from Fordham's commentaries, obituaries, papers and reviews which capture not only the development of Fordham as a thinker but also his character. There is discussion of his reviews of Melanie Klein's Envy and Gratitude and manuscripts by Erich Neumann. A reminiscence of Fordham as supervisor is recounted.

The potential role of oral pH in the persistence of Trichomonas gallinae in Cooper's Hawks (Accipiter cooperii).

Trichomoniasis, caused by the protozoan Trichomonas gallinae, affects a variety of species worldwide including avivorious raptors. Existing information suggests that the disease is most prevalent in young birds, and differential susceptibility to trichomoniasis among individuals in different age groups was documented in Cooper's Hawks (Accipiter cooperii) nesting in Tucson, Arizona. In that population, 85% of nestling Cooper's Hawks had T. gallinae in their oral cavity, compared to only 1% of breeding-age hawks. Trichomonads generally are sensitive to environmental pH and we explored the possibility that differences in oral pH may contribute to the differential prevalence of infection between age groups. We measured the pH of the fluid in the oral cavity in 375 Cooper's Hawks from three age groups (nestlings, fledglings, and breeding age) in Tucson, Arizona, in 2010 and 2011 and clinically tested for T. gallinae in a subsample of hawks. Oral pH of nestlings (∼ 6.8) was 7.3 times less acidic than in fledgling or breeding Cooper's Hawks (∼ 6.1). The incidence of T. gallinae was higher in nestlings (16%) than in either fledglings or breeding hawks (0%). Our findings indicate that oral pH becomes more acidic in Cooper's Hawks soon after they leave the nest. Trichomonas gallinae thrives when pH is between 6.5 and 7.5 (optimum 7.2), but is less viable in more acidic conditions. Higher levels of acidity in the oral cavity of fledglings and breeding Cooper's Hawks may reduce their susceptibility to trichomoniasis, and play a role in the differential prevalence of infection among age groups.

End notes: two unpublished presentations by Michael Fordham.

Following the publication in this journal of two of Fordham's unpublished papers selected by James Astor (2010, 55, 5), the editors have asked me to select a further two. I have chosen two clinical pieces, one clinical notes and the other notes that refine his previous thinking, which Fordham wrote at the end of his life. Both are examples of the way Fordham continued throughout his analytic work to turn to patients as his primary source of learning. Fordham presented the first piece, 'A case study', to Parkside Clinic in 1988. Its subject is his last child patient, a nine-year-old boy with behaviour problems that destroyed the analytic frame. The second is clearly for an SAP (Society of Analytical Psychology) audience and written probably around 1992-93. It is titled 'Some comments on transference and countertransference' and contains material from the patient who has become known through papers in this journal as 'K'. The two pieces are presented together within a commentary rather than separately with footnotes, in order to provide some context for Fordham's thinking in his late years.

Reflections on research and learning from the patient: the art and science of what we do.

Over three decades ago, John Bowlby argued for psychoanalysis to seek beyond its own parameters if it was to maintain its claim to be a science. Since then there has been a wealth of relevant research from various fields. While this has been instrumental in the development of my own work, this paper concerns learning from the patient. The paper begins with a premise: interpretative analytic work requires three-dimensionality (self, other and object). Although interpretative work may be ingrained in our professional identity, this triangulation may or may not exist in our patients in any stable way. The paper continues with a brief developmental account of how early archetypally-shaped shifts in the infant's field of interest establish the experiential components of three-dimensionality. From there, observational and clinical material with a toddler and a young boy describe how early relational deficits hindered their capacities for three-dimensionality. Yet both were able to engage with the therapist and to become active in the creation of three-dimensionality within their own minds. Implied in this work are considerations for working with patients for whom interpretations do not work. Michael Fordham's comments on 'working out of the self' are linked with the art of what we do.

Repertoire development and the control of cytotoxic/effector function in human gammadelta T cells.

T cells develop into two major populations distinguished by their T cell receptor (TCR) chains. Cells with the alphabeta TCR generally express CD4 or CD8 lineage markers and mostly fall into helper or cytotoxic/effector subsets. Cells expressing the alternate gammadelta TCR in humans generally do not express lineage markers, do not require MHC for antigen presentation, and recognize nonpeptidic antigens. We are interested in the dominant Vgamma2Vdelta2+ T cell subset in human peripheral blood and the control of effector function in this population. We review the literature on gammadelta T cell generation and repertoire selection, along with recent work on CD56 expression and defining a cytotoxic/effector lineage within the phosphoantigen-reactive Vgamma2Vdelta2 cells. A unique mechanism for MHC-independent repertoire selection is linked to the control of effector function that is vital to the role for gammadelta T cells in tumor surveillance. Better understanding of these mechanisms will improve our ability to exploit this population for tumor immunotherapy.

Control of CD56 expression and tumor cell cytotoxicity in human Vgamma2Vdelta2 T cells.

BACKGROUND: In lymphocyte subsets, expression of CD56 (neural cell adhesion molecule-1) correlates with cytotoxic effector activity. For cells bearing the Vgamma2Vdelta2 T cell receptor, isoprenoid pyrophosphate stimulation leads to uniform activation and proliferation, but only a fraction of cells express CD56 and display potent cytotoxic activity against tumor cells. Our goal was to show whether CD56 expression was regulated stochastically, similar to conventional activation antigens, or whether CD56 defined a lineage of cells committed to the cytotoxic phenotype. RESULTS: Tracking individual cell clones defined by their Vgamma2 chain CDR3 region sequences, we found that CD56 was expressed on precursor cytotoxic T cells already present in the population irrespective of their capacity to proliferate after antigen stimulation. Public T cell receptor sequences found in the CD56+ subset from one individual might appear in the CD56- subset of another donor. The commitment of individual clones to CD56+ or CD56- lineages was stable for each donor over a 1 year interval. CONCLUSION: The ability to express CD56 was not predicted by TCR sequence or by the strength of signal received by the TCR. For gammadelta T cells, cytotoxic effector function is acquired when cytotoxic precursors within the population are stimulated to proliferate and express CD56. Expression of CD56 defines a committed lineage to the cytotoxic phenotype.

Evaluation of the pathogenesis of decreasing CD4(+) T cell counts in human immunodeficiency virus type 1-infected patients receiving successfully suppressive antiretroviral therapy.

Most human immunodeficiency virus (HIV)-infected individuals experience increases in peripheral CD4(+) T cell counts with suppressive antiretroviral therapy (ART) that achieves plasma HIV RNA levels that are less than the limit of detection. However, some individuals experience decreasing CD4(+) T cell counts despite suppression of plasma viremia. We evaluated 4 patients with a history of CD4(+) T cell decline despite successfully suppressive ART, from a median of 719 cells/mm(3) (range, 360-1141 cells/mm(3)) to 227 cells/mm(3) (range, 174-311 cells/mm(3)) over a period of 18-24 months; 3 of the patients were receiving tenofovir and didanosine, which may have contributed to this decrease. There was no evidence of HIV replication, nor of antiretroviral drug resistance in the blood or lymphoid tissue, or increased proliferation or decreased thymic production of naive CD4(+) T cells. All 4 patients had significant fibrosis of the T cell zone of lymphoid tissue, which appeared to be an important factor in the failure to reconstitute T cells.

The 'self' in analytical psychology: the function of the 'central archetype' within Fordham's model.

This paper concerns the self as Fordham came to conceive it after a conceptual analysis of Jung's use of the term. Fordham identified a contradiction in Jung's usage, and resolved it by reserving 'self' for a definition of the psychosomatic entirety of the individual, and using a separate term for referring to expressions of the self in human experience (e.g. symbols). Fordham tentatively suggested that the latter be termed the 'central archetype', although this was neither developed nor dropped. I explore the value of this term from a developmental perspective and, more specifically in terms of the deintegration of psyche out of an early psychosomatic unity. This draws upon infant research and an observation of a 14-month old boy. Finally, further developments are briefly described and illustrated, whereby pre-symbolic expressions of the central archetype become symbolic and come to reflect what was for Jung, the 'ultimate', 'Formation, Transformation, Eternal Mind's eternal recreation'.

Virological outcome after structured interruption of antiretroviral therapy for human immunodeficiency virus infection is associated with the functional profile of virus-specific CD8+ T cells.

A clear understanding of the antiviral effects of CD8(+) T cells in the context of chronic human immunodeficiency virus (HIV) infection is critical for the development of prophylactic vaccines and therapeutics designed to support T-cell-mediated immunity. However, defining the potential correlates of effective CD8(+) T-cell immunity has proven difficult; notably, comprehensive analyses have demonstrated that the size and shape of the CD8(+) T-cell response are not necessarily indicative of efficacy determined by measures of plasma viral load. Here, we conducted a detailed quantitative and qualitative analysis of CD8(+) T-cell responses to autologous virus in a cohort of six HIV-infected individuals with a history of structured interruption of antiretroviral therapy (ART) (SIT). The magnitude and breadth of the HIV-specific response did not, by themselves, explain the changes observed in plasma virus levels after the cessation of ART. Furthermore, mutational escape from targeted epitopes could not account for the differential virological outcomes in this cohort. However, the functionality of HIV-specific CD8(+) T-cell populations upon antigen encounter, determined by the simultaneous and independent measurement of five CD8(+) T-cell functions (degranulation and gamma interferon, macrophage inflammatory protein 1beta, tumor necrosis factor alpha, and interleukin-2 levels) reflected the emergent level of plasma virus, with multiple functions being elicited in those individuals with lower levels of viremia after SIT. These data show that the quality of the HIV-specific CD8(+) T-cell response, rather than the quantity, is associated with the dynamics of viral replication in the absence of ART and suggest that the effects of SIT can be assessed by measuring the functional profile of HIV-specific CD8(+) T cells.