Internet Applications for Computational Biology, the CMISS Web Browser Extension and and Use in Education

The Internet is becoming increasingly accessible and new technologies are enabling the delivery of more features to end users. It is therefore increasingly compelling to develop technology to facilitate the delivery of educational content and computational tools via the Internet. Here we report on the Internet enabling of the CMISS package as a Web browser extension, and its use in a custom online teaching application for medical students.

Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus

Idiopathic congenital nystagmus is characterized by involuntary, periodic, predominantly horizontal oscillations of both eyes. We identified 22 mutations in FRMD7 in 26 families with X-linked idiopathic congenital nystagmus. Screening of 42 singleton cases of idiopathic congenital nystagmus (28 male, 14 females) yielded three mutations (7%). We found restricted expression of FRMD7 in human embryonic brain and developing neural retina, suggesting a specific role in the control of eye movement and gaze stability.

Differential roles of CD8+ and CD8- T lymphocytes in corneal allograft rejection in 'high-risk' hosts

We examined the role of perforin and FasL in corneal allograft rejection mediated by CD8+ and CD8 T cells. BALB/c corneas were transplanted orthotopically into vascularized, 'high-risk' graft beds in C57BL/6 mice, perforin knockout mice and FasL-defective gld/gld mice. CD8+ and CD8 T cells were collected following graft rejection and adoptively transferred to SCID mice, which were then challenged with BALB/c corneal allografts. In every case, CD8 T cells could mediate graft rejection when adoptively transferred to SCID mice that received BALB/c corneal allografts. Although CD8+ T cells also mediated graft rejection, the tempo was slower. Moreover, CD8+ T cells collected FasL-defective donors that had rejected corneal allografts, mediated corneal allograft rejection in only 50% of the SCID mice that received the adoptively transferred cells. In some cases, CD8+ T-cell-mediated rejection occurred in the absence of delayed-type hypersensitivity and cytotoxic T-lymphocyte activity, but was associated with CD8+ T-cell-mediated apoptosis of BALB/c corneal cells in vitro. The results demonstrate the redundancy in immune mechanisms of corneal allograft rejection. Either CD8+ or CD8 T cells can produce corneal allograft rejection, however functional FasL is necessary for optimal rejection, even in a high-risk setting.

A comparison of corrected serum calcium levels to ionized calcium levels among critically ill surgical patients

BACKGROUND

Aberrations in calcium homeostasis are common in critically ill patients. The proper method to evaluate this issue in surgical patients has not been completely defined.

METHODS

Medical records of patients admitted to a university-affiliated, tertiary-care surgical intensive care unit were retrospectively reviewed. Calcium status was evaluated by ionized levels and as a function of serum calcium levels corrected for albumin aberrations.

RESULTS

Corrected serum calcium values failed to accurately classify calcium status in 38% of cases. The sensitivity and specificity of the corrected serum calcium formula to evaluate hypocalcemia were 53% and 85%, respectively. Corrected serum values underestimated the prevalence of hypocalcemia and overestimated the prevalence of normocalcemia. No factors were able to discern which patients could be evaluated by corrected serum calcium levels.

CONCLUSIONS

Calcium homeostasis should be evaluated by ionized calcium levels rather than as a function of serum calcium and albumin levels.

Relationship between symptoms and disordered continence mechanisms in women with idiopathic faecal incontinence

BACKGROUND AND AIMS

Anal sphincter weakness and rectal sensory disturbances contribute to faecal incontinence (FI). Our aims were to investigate the relationship between symptoms, risk factors, and disordered anorectal and pelvic floor functions in FI.

METHODS

In 52 women with "idiopathic" FI and 21 age matched asymptomatic women, we assessed symptoms by standardised questionnaire, anal pressures by manometry, anal sphincter appearance by endoanal ultrasound and magnetic resonance imaging (MRI), pelvic floor motion by dynamic MRI, and rectal compliance and sensation by a barostat.

RESULTS

The prevalence of anal sphincter injury (by imaging), reduced anal resting pressure (35% of FI), and reduced squeeze pressures (73% of FI) was higher in FI compared with controls. Puborectalis atrophy (by MRI) was associated (p<0.05) with FI and with impaired anorectal motion during pelvic floor contraction. Volume and pressure thresholds for the desire to defecate were lower, indicating rectal hypersensitivity, in FI. The rectal volume at maximum tolerated pressure (that is, rectal capacity) was reduced in 25% of FI; this volume was associated with the symptom of urge FI (p<0.01) and rectal hypersensitivity (p = 0.02). A combination of predictors (age, body mass index, symptoms, obstetric history, and anal sphincter appearance) explained a substantial proportion of the interindividual variation in anal squeeze pressure (45%) and rectal capacity (35%).

CONCLUSIONS

Idiopathic FI in women is a multifactorial disorder resulting from one or more of the following: a disordered pelvic barrier (anal sphincters and puborectalis), or rectal capacity or sensation.

Transcriptional regulation of components of the type III secretion system and effectors in Pseudomonas syringae pv. phaseolicola

Quantitative real-time polymerase chain reaction was used with specific TaqMan probes to examine transcription of selected hrp and effector genes in Pseudomonas syringae pv. phaseolicola strains 1448A (race 6) and 1449B (race 7). Transcripts examined were from genes encoding the regulators hrpR and hrpL, core structural components of the type III secretion system (TTSS) hrcC, hrcJ, hrcN, hrcU, and hrpA; the first open-reading frame of each hrp operon, including hrpF, hrpJ, hrpP, and hrpY, and also secreted effectors hrpZ, avrPphE, avrPphF, and virPphA. All genes were induced by incubation in a minimal medium and showed patterns of expression indicating regulation by HrpRS and HrpL. Basal mRNA levels and the timing of accumulation of transcripts after induction differed significantly, suggesting the operation of additional regulatory elements. However, no clear transcriptional hierarchy emerged to explain the ordered construction of the TTSS. Quantitative analysis confirmed that the rates and levels of transcript accumulation within the first 2 h after inoculation were considerably higher in planta than in vitro, and indicated that plant cell wall contact may enhance transcription of TTSS and effector genes in P. syringae pv. phaseolicola. The low-abundance hrcU mRNA had a half-life of 16.5 min, whereas other transcripts had half-lives between 3 and 8 min.