The evolution and mutational robustness of chromatin accessibility in Drosophila

BACKGROUND

The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila.

RESULTS

We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that our models generalize well across substantially evolutionarily diverged species of insects, implying that the sequence determinants of accessibility are highly conserved. Using our model to examine species-specific gains in accessibility, we find evidence suggesting that these regions may be ancestrally poised for evolution. Using in silico mutagenesis, we show that accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that accessibility is mutationally robust. Subsequently, we show that accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. Conversely, simulations under strong selection demonstrate that accessibility can be extremely malleable despite its robustness. Finally, we identify motifs predictive of accessibility, recovering both novel and previously known motifs.

CONCLUSIONS

These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks to explore fundamental questions in regulatory genomics and evolution.

The evolution and mutational robustness of chromatin accessibility in Drosophila

The evolution of regulatory regions in the genome plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems has made it difficult to understand the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different tissues of Drosophila. We train hybrid convolution-attention neural networks to accurately predict ATAC-seq peaks using only local DNA sequences as input. We show that a model trained in one species has nearly identical performance when tested in another species, implying that the sequence determinants of accessibility are highly conserved. Indeed, model performance remains excellent even in distantly-related species. By using our model to examine species-specific gains in chromatin accessibility, we find that their orthologous inaccessible regions in other species have surprisingly similar model outputs, suggesting that these regions may be ancestrally poised for evolution. We then use in silico saturation mutagenesis to reveal evidence of selective constraint acting specifically on inaccessible chromatin regions. We further show that chromatin accessibility can be accurately predicted from short subsequences in each example. However, in silico knock-out of these sequences does not qualitatively impair classification, implying that chromatin accessibility is mutationally robust. Subsequently, we demonstrate that chromatin accessibility is predicted to be robust to large-scale random mutation even in the absence of selection. We also perform in silico evolution experiments under the regime of strong selection and weak mutation (SSWM) and show that chromatin accessibility can be extremely malleable despite its mutational robustness. However, selection acting in different directions in a tissue-specific manner can substantially slow adaptation. Finally, we identify motifs predictive of chromatin accessibility and recover motifs corresponding to known chromatin accessibility activators and repressors. These results demonstrate the conservation of the sequence determinants of accessibility and the general robustness of chromatin accessibility, as well as the power of deep neural networks as tools to answer fundamental questions in regulatory genomics and evolution.

Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads

Evolutionarily young genes are usually preferentially expressed in the testis across species. Although it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using Drosophila gene expression data, we confirmed previous findings that younger genes are disproportionately testis biased and older genes are disproportionately ovary biased. We found that the relationship between gene age and expression is stronger in the ovary than any other tissue and weakest in testis. We performed ATAC-seq on Drosophila testis and found that although genes of all ages are more likely to have open promoter chromatin in testis than in ovary, promoter chromatin alone does not explain the ovary bias of older genes. Instead, we found that upstream transcription factor (TF) expression is highly predictive of gene expression in ovary but not in testis. In the ovary, TF expression is more predictive of gene expression than open promoter chromatin, whereas testis gene expression is similarly influenced by both TF expression and open promoter chromatin. We propose that the testis is uniquely able to express younger genes controlled by relatively few TFs, whereas older genes with more TF partners are broadly expressed with peak expression most likely in the ovary. The testis allows widespread baseline expression that is relatively unresponsive to regulatory changes, whereas the ovary transcriptome is more responsive to trans-regulation and has a higher ceiling for gene expression.

Fast-ion orbit sensitivity of neutron emission spectroscopy diagnostics

Fast ions in fusion plasmas often leave characteristic signatures in the plasma neutron emission. Measurements of this emission are subject to the phase-space sensitivity of the diagnostic, which can be mapped using weight functions. In this paper, we present orbit weight functions for the TOFOR and NE213 neutron diagnostics at the Joint European Torus, mapping their phase-space sensitivity in 3D orbit space. Both diagnostics are highly sensitive to fast ions that spend a relatively large fraction of their orbit transit times inside the viewing cone of the diagnostic. For most neutron energies, TOFOR is found to be relatively sensitive to potato orbits and heavily localized counter-passing orbits, as well as trapped orbits whose "banana tips" are inside the viewing cone of TOFOR. For the NE213-scintillator, the sensitivity is found to be relatively high for stagnation orbits.

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

The testis is a peculiar tissue in many respects. It shows patterns of rapid gene evolution and provides a hotspot for the origination of genetic novelties such as de novo genes, duplications and mutations. To investigate the expression patterns of genetic novelties across cell types, we performed single-cell RNA-sequencing of adult Drosophila testis. We found that new genes were expressed in various cell types, the patterns of which may be influenced by their mode of origination. In particular, lineage-specific de novo genes are commonly expressed in early spermatocytes, while young duplicated genes are often bimodally expressed. Analysis of germline substitutions suggests that spermatogenesis is a highly reparative process, with the mutational load of germ cells decreasing as spermatogenesis progresses. By elucidating the distribution of genetic novelties across spermatogenesis, this study provides a deeper understanding of how the testis maintains its core reproductive function while being a hotbed of evolutionary innovation.

Peripartum interventions resulting in reduced perinatal mortality rates, and birth asphyxia rates, over 18 years in a tertiary centre in South India: a retrospective study

OBJECTIVE

To study the changes in the rates of perinatal mortality, birth asphyxia, and caesarean sections in relation to interventions implemented over the past 18 years, in a tertiary centre in South India.

DESIGN

Retrospective study.

SETTING

Labour and maternity unit of a tertiary centre in South India.

POPULATION OR SAMPLE

Women who gave birth between 2000 and 2018.

METHODS

Information from perinatal audits, chart reviews, and data retrieved from the electronic database were used. Interventions implemented during this time period were audits and training, obstetric re-organisation, and minor changes in staffing and infrastructure.

MAIN OUTCOME MEASURES

Main outcome measures were perinatal mortality rate, birth asphyxia rate, and caesarean section rate.

RESULTS

Perinatal mortality rate decreased from 44 per 1000 births in 2000 to 16.4 per 1000 births in 2018 (P < 0.001). The rates of babies born with birth asphyxia requiring admission to the neonatal unit decreased from 24 per 1000 births in 2001 to 0.7 per 1000 births in 2018 (P < 0.00001). The overall caesarean section rate was maintained close to 30%.

CONCLUSION

In a large tertiary hospital in South India, with 14 000 deliveries per year, a policy of rigorous audits of stillbirths and birth asphyxia, electronic fetal monitoring, and the introduction of standardised criteria for trial of scar, reduced the perinatal mortality and the rate of babies born with birth asphyxia over the past 18 years, without an increase in the caesarean section rate.

TWEETABLE ABSTRACT

Rigorous perinatal audits with training in fetal cardiotocography, decreased birth asphyxia, without a major increase in caesarean rates.

IgG4-related disease involving the esophagus: a clinicopathological study

Immunoglobulin G4 (IgG4)-related disease is a recently coined systemic disease characterized by specific histopathologic findings of an intense lymphoplasmacytic infiltrate, storiform fibrosis, and obliterative phlebitis in the presence of predominant IgG4-positive plasma cells. Although IgG4-related disease has been described in many organs, involvement of the esophagus is very rare. In this study, we describe the clinicopathologic characteristics of eight patients with IgG4-related esophagitis. We evaluated chronic esophagitis specimens with lymphoplasmacytic infiltrate obtained over the past 6 years (from January 2011 to February 2017) using a chart review, pathologic examination, and IgG4 immunohistochemical staining. The diagnoses of the specimens were either confirmed as IgG4-related esophagitis (IgG4-RE) or chronic esophagitis, not otherwise specified (CENOS), and the clinicopathologic data from each group were compared. Eight patients were diagnosed with IgG4-RE and 10 controls were identified and diagnosed with CENOS. In the IgG4-RE group, esophageal strictures were identified in three patients, two patients had postmyotomy treated achalasia, one patient had erosive esophagitis and another presented with an esophageal nodule. Only one patient had an unremarkable mucosa on endoscopy. In the CENOS group, four patients had esophageal strictures, six had erosive esophagitis, one patient had mild esophagitis. The IgG4-RE group had significantly higher numbers of IgG4-positive plasma cells (66.9 ± 21.9 vs. 4.7 ± 2.4 per high power field; P< 0.001) and a greater IgG4: IgG ratio 0.76 ± 0.13 vs. 0.06 ± 0.05; P< 0.001) when compared to CENOS patients. Two of the patients with recurrent esophageal strictures in the IgG4-RE group showed initial response to steroid therapy and are currently on immunosuppressive therapy which has significantly reduced the need for multiple esophageal dilatations. The presentation of IgG4-related esophageal disease can vary and the key to diagnosis is dependent on histopathology. These observations highlight the need for IgG4 immunohistochemical staining of esophageal biopsies especially in patients with mucosal ulceration, chronic inflammation, and plasmacytosis on biopsy. This will prevent unwarranted esophagectomies and failed medical treatment due to lack of recognition of this entity.

Venous thromboembolism after total knee replacement or total hip replacement: what can be learnt from root-cause analysis?

INTRODUCTION Because of the high risk of venous thromboembolism (VTE) in total hip replacement (THR) and total knee replacement (TKR), guidelines are used widely to enhance effective (yet safe) prophylaxis. If patients develop VTEs despite use of such guidelines, then the reasons are that the guidelines were: (i) followed but the VTE occurred anyway; (ii) not implemented appropriately. All VTEs are assessed routinely by root-cause analysis (RCA). METHODS The records and subsequent RCA reports for each patient who experienced clinically significant VTE after THR or TKR were reviewed. We established adherence to the guidelines (deemed to be 'unavoidable' with scope to improve the guidelines) and non-adherence (deemed to be 'avoidable' with scope to improve implementation). RESULTS Of 2,214 patients undergoing THR (n=1,330) or TKR (n=884), 25 (1.13%) experienced VTE. Four THR patients experienced VTE (2 of which were avoidable) and 21 TKR patients experienced VTE (5 of which were avoidable). There were significantly more VTEs in TKR patients than THR patients (p<0.0001). CONCLUSIONS A proportion of patients will experience VTE even if guidelines are followed (a baseline effect). Administration of chemical prophylaxis earlier might reduce this baseline effect further. This approach should be taken cautiously with due respect for the alternative risk of bleeding. Improvement in hospital routine may reduce the risk of VTE yet further.

Oral administration of Moringa oleifera oil but not coconut oil prevents mercury-induced testicular toxicity in rats

This study was conducted to compare the effects of administration of coconut oil (CO) and Moringa oleifera oil (MO) on testicular oxidative stress, sperm quality and steroidogenesis parameters in rats treated with mercury chloride (HgCl₂ ). After 15 days of oral administration of CO (2 ml kg^-1 body weight) and MO (2 ml kg^-1 body weight) along with intraperitoneal (i.p.) administration of HgCl₂ (5 mg kg^-1 body weight) alone or in combination, we found that CO treatment did not protect against HgCl₂ -induced poor sperm quality (motility, count) as well as decreased testosterone level and 17β-hydroxysteroid dehydrogenase (17β-HSD) activity. Treatment with CO alone decreased glutathione (GSH), and glutathione peroxidase (GSH-Px) activities and increased malondialdehyde (MDA) level in rat's testis, whereas MO did not change these parameters. Cotreatment with MO prevented HgCl₂ -induced testicular catalase (CAT) and superoxide dismutase (SOD) activities, poor sperm quality and low testosterone level and also blocks the adverse effect of CO+HgCl₂ (2 ml kg^-1 body weight + 5 mg kg^-1 body weight) on the investigated endpoints. In conclusion, MO and not CO decreased the deleterious effects of HgCl₂ on sperm quality and steroidogenesis in rats and also strengthen the antioxidant defence of the testes. Therefore, MO is beneficial as an antioxidant in HgCl₂ -induced oxidative damage.

Nest location influences hatching success in the Socotra Cormorant (Phalacrocorax nigrogularis) on Siniya Island, United Arab Emirates

Context Nest location is an important determinant of reproductive success in many seabirds. Better understanding of breeding ecology of threatened seabirds could help in their conservation. Aims We evaluated nest location and reproductive success in the globally Vulnerable, regionally endemic, Socotra cormorants on Siniya Island, United Arab Emirates, in relation to multiple habitat factors to assess the relative influence of each. Methods We measured hatching success, as an indication of reproductive success, on 14 study plots during the 2011–12 breeding season. We measured distances from each study plot to the nearest tree, road, predation area, sandy beach and lagoon. We used multiple logistic regression to determine the extent to which these explanatory factors influenced hatching success. We used an information theoretic approach to select the best model. Key results Hatching success was significantly related to tree cover, distance from beach and distance from heavily depredated areas (AICc weight = 0.613). Nests were significantly deeper (13.14 ± 0.35 cm) in unshaded areas compared with areas shaded by trees (10.8 ± 0.31 cm) (ANOVA: F2,12 = 24.93, P < 0.001). Conclusions Thus, we conclude that shade provided by planted non-native trees is an important factor affecting nest location and hatching success. Deeper nests could aid incubation by lowering nest temperatures during peak incubation periods (August) when temperatures may exceed 48°C. Heavy predation pressure is affecting hatching success. Wind action could be preventing nesting near the sandy beach. Implications Planted non-native trees are advantageous to breeding Socotra cormorants, although planting trees is not advocated. High predation pressure from feral cats and red foxes is reducing hatching success of Socotra cormorants on the largest known colony in the United Arab Emirates. Feral cats should be eradicated whereas the red foxes could be managed as a precautionary measure to ensure the continued survival of this threatened seabird.

Thromboembolic complications of thyroid storm

Thyroid storm is a rare but potentially life-threatening complication of hyperthyroidism. Early recognition and prompt treatment are essential. Atrial fibrillation can occur in up to 40% of patients with thyroid storm. Studies have shown that hyperthyroidism increases the risk of thromboembolic events. There is no consensus with regard to the initiation of anticoagulation for atrial fibrillation in severe thyrotoxicosis. Anticoagulation is not routinely initiated if the risk is low on a CHADS2 score; however, this should be considered in patients with thyroid storm or severe thyrotoxicosis with impending storm irrespective of the CHADS2 risk, as it appears to increase the risk of thromboembolic episodes. Herein, we describe a case of thyroid storm complicated by massive pulmonary embolism.

Spray application of Bacillus thuringiensis israelensis (Bti strain AM65-52) against Aedes aegypti (L.) and Ae. albopictus Skuse populations and impact on dengue transmission in a dengue endemic residential site in Malaysia

A one year study was conducted to evaluate the impact of spray application of Bacillus thuringiensis israelensis (Bti), strain AM65-52 on vector populations and dengue transmission in a dengue endemic state in Malaysia. Residential sites with similar populations of Aedes aegypti (L.) and Aedes albopictus Skuse were studied. One site was treated with spray application of Bti into all outdoor target vector habitats, which consisted of natural and artificial containers. The other site was not treated. The impact of spray application was measured with an indoor and outdoor ovitrap index (OI) and epidemiologic data. Significant reductions in both Ae. aegypti and Ae. albopictus, OI were observed both indoors and outdoors, in treated sites compared to untreated sites (p < 0.05). OI reduction was achieved over time in the treated area. The OI was suppressed to below 10%. This was maintained for 4 weeks into the post-treatment phase. The outdoor OI at the untreated site remained at more than 40% for 38 weeks during the evaluation period. One dengue case occurred at the Bti treatment site at the beginning of the treatment phase, but no further cases were detected during the remainder of the treatment phase. However, there was an ongoing dengue outbreak in the untreated area with 15 serologically confirmed cases during weeks 37-54. Intensive fogging operations with pyrethroids at the untreated (Bti) site had a positive impact on Ae. albopictus, but not on Ae. aegypti.

A conserved F box regulatory complex controls proteasome activity in Drosophila

The ubiquitin-proteasome system catalyzes the degradation of intracellular proteins. Although ubiquitination of proteins determines their stabilities, there is growing evidence that proteasome function is also regulated. We report the functional characterization of a conserved proteasomal regulatory complex. We identified DmPI31 as a binding partner of the F box protein Nutcracker, a component of an SCF ubiquitin ligase (E3) required for caspase activation during sperm differentiation in Drosophila. DmPI31 binds Nutcracker via a conserved mechanism that is also used by mammalian FBXO7 and PI31. Nutcracker promotes DmPI31 stability, which is necessary for caspase activation, proteasome function, and sperm differentiation. DmPI31 can activate 26S proteasomes in vitro, and increasing DmPI31 levels suppresses defects caused by diminished proteasome activity in vivo. Furthermore, loss of DmPI31 function causes lethality, cell-cycle abnormalities, and defects in protein degradation, demonstrating that DmPI31 is physiologically required for normal proteasome activity.

Another tier for caspase regulation: IAPs as NEDD8 E3 ligases

Many inhibitor of apoptosis proteins (IAPs) function as E3 ligases to ubiquitinate important cell death proteins, including caspases. Broemer et al. (2010) report recently in Molecular Cell that IAPs can also inhibit caspases by promoting conjugation of the UBL NEDD8.

Susceptibility of field-collected Aedes aegypti (L.) (Diptera: Culicidae) to Bacillus thuringiensis israelensis and temephos

The susceptibility status of field-collected Aedes aegypti (L.) from a dengue endemic area to Bacillus thuringiensis israelensis (Bti) and temephos was determined. Since August 2007, biweekly ovitrap surveillance (OS) was conducted for 12 mo in 2 sites, A & B, in Shah Alam, Selangor. Site A was treated with a Bti formulation, VectoBac® WG at 500 g/ha, from December 2007 - June 2008 while Site B was subjected to routine dengue vector control activities conducted by the local municipality. Aedes aegypti larvae collected from OS in both sites were bred until F3 and evaluated for their susceptibility. The larvae were pooled according to 3 time periods, which corresponded to Bti treatment phases in site A: August - November 2007 (Bti pre-treatment phase); December 2007 - June 2008 (Bti treatment phase); and July - September 2008 (Bti post-treatment phase). Larvae were bioassayed against Bti or temephos in accordance with WHO standard methods. Larvae collected from Site A was resistant to temephos, while incipient temephos resistant was detected in Site B throughout the study using WHO diagnostic dosage of 0.02 mg/L. The LC50 of temephos ranged between 0.007040 - 0.03799 mg/L throughout the year in both sites. Resistance ratios (LC50) indicated that temephos resistance increased with time, from 1.2 - 6.7 folds. The LC50 of Ae. aegypti larvae to Bti ranged between 0.08890 - 0.1814 mg/L throughout the year in both sites, showing uniform susceptibility of field larvae to Bti, in spite of Site A receiving 18 Bti treatments over a period of 7 mo. No cross-resistance of Ae. aegypti larvae from temephos to Bti was detected.

Preventing Alzheimer's disease and cognitive decline

OBJECTIVES

To assess whether previous research on purported risk or protective factors for Alzheimer's disease (AD) and cognitive decline is of sufficient strength to warrant specific recommendations for behavioral, lifestyle, or pharmaceutical interventions/modifications targeted to these endpoints.

DATA SOURCES

MEDLINE and the Cochrane Database of Systematic Reviews. Additional studies were identified from reference lists and technical experts.

REVIEW METHODS

A group of experts in the field developed the list of factors to be evaluated in preparation for an upcoming National Institutes of Health (NIH) Office of Medical Applications of Research (OMAR) State-of-the-Science Conference addressing the prevention of AD and cognitive decline. We grouped the factors into the following categories: nutritional factors, medical conditions and prescription and non-prescription medications, social/economic/behavioral factors, toxic environmental factors, and genetics. Outcomes of interest were the development of AD or cognitive decline. Both observational and intervention studies were evaluated. Studies were evaluated for eligibility and quality, and data were abstracted on study design, demographics, intervention or predictor factor, and cognitive outcomes.

RESULTS

A total of 25 systematic reviews and 250 primary research studies were included. Only a few factors showed a consistent association with AD or cognitive decline across multiple studies, including both observational studies and randomized controlled trials (when available). Such factors associated with increased risk of AD and cognitive decline were: diabetes, epsilon 4 allele of the apolipoprotein E gene (APOE e4), smoking, and depression. Factors showing a fairly consistent association with decreased risk of AD and cognitive decline were: cognitive engagement and physical activities. A consistent association does not imply that findings were robust, as the data were often limited, and the quality of evidence was typically low. In addition, the modification of risk for reported associations was typically small to moderate for AD, and small for cognitive decline. Some of the factors that did not show an association with AD or cognitive decline in this review may still play an influential role in late-life cognition, but there was not sufficient evidence to draw this conclusion. Many of the factors evaluated are not amenable to randomization, so rigorous observational studies are required to assess their effect on AD and cognitive decline.

CONCLUSIONS

The current research on the list of putative risk or protective factors is largely inadequate to confidently assess their association with AD or cognitive decline. Further research that addresses the limitations of existing studies is needed prior to be able to make recommendations on interventions.

Circulating microRNAs as potential blood-based biomarkers for detection of colorectal cancer

e15040

Background: Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide. While there is a strong correlation between stage and prognosis in this disease, current screening methods for CRC have significant limitations, and newer technological approaches are desired. Circulating nucleic acids in body fluids have been studied as a source for diagnostic information and for cancer screening, yet the potential of microRNAs, a family of small non-coding regulatory RNAs, has not yet been thoroughly explored. Here we investigated the utility of microRNAs as potential serum biomarkers for early detection of CRC. Methods: We developed protocols for extracting and quantifying microRNA levels in serum. Serum levels of more than 350 microRNAs were measured using qRT-PCR on samples from 10 healthy controls and 10 CRC patients. Most microRNAs showed consistent levels across different individuals. A subset of microRNAs had significant differences in abundance between the two groups and was studied on a larger cohort of 118 patients and controls. Results: We initially identified a subset of microRNAs that showed significant differential abundance between sera of CRC patients and controls. Measuring the serum levels of 22 microRNAs on a cohort of 118 patients and controls, we showed that levels of circulating microRNAs can be very informative in the identification of CRC. Conclusions: The results demonstrate the potential of the microRNA processing and analysis methods that we developed. Certain microRNAs were found in different amounts in sera of CRC patients compared to healthy controls. Thus, circulating microRNAs represent promising candidates for diagnostic biomarkers in CRC.

[Table: see text]

Drosophila Past1 is involved in endocytosis and is required for germline development and survival of the adult fly

Endocytosis, which is a key process in eukaryotic cells, has a central role in maintaining cellular homeostasis, nutrient uptake, development and downregulation of signal transduction. This complex process depends on several protein-protein interactions mediated by specific modules. One such module is the EH domain. The EH-domain-containing proteins comprise a family that includes four vertebrate members (EHD1-EHD4) and one Drosophila ortholog, Past1. We used Drosophila as a model to understand the physiological role of this family of proteins. We observed that the two predicted Past1 transcripts are differentially expressed both temporally and spatially during the life cycle of the fly. Endogenous Past1 as well as Past1A and Past1B, expressed from plasmids, were localized mainly to the membrane of Drosophila-derived cells. We generated mutants in the Past1 gene by excising a P-element inserted in it. The Past1 mutants reached adulthood but died precociously. They were temperature sensitive and infertile because of lesions in the reproductive system. Garland cells that originated from Past1 mutants exhibited a marked decrease in their ability to endocytose fluorescently labeled avidin. Genetic interaction was found between Past1 and members of the Notch signaling pathway, suggesting a role for Past1 in this developmentally crucial signaling pathway.

AtEHDs in endocytosis

Endocytosis regulates many important and diverse processes in eukaryotic life. EH domain containing proteins function as regulators of endocytosis through protein-protein interactions. Several interactors of mammalian EHDs were identified, including clathrin machinery components. The four human EHD proteins share high homology at the protein level and possess similar domains, but appear to be involved in different stages of intracellular trafficking. EHD1 regulates recycling through the endocytic recycling compartment (ERC). EHD2 has been found to inhibit internalization in mammalians when overexpressed.We have recently investigated the importance of EH domain containing proteins in plant endocytosis. We were able to show that both of the Arabidopsis EHD homologs, termed AtEHD1 and AtEHD2, play important roles in plant endocytosis. Knockdown of AtEHD1 delayed internalization, and overexpression of AtEHD2 inhibited endocytosis. Thus, the function of plant EHDs is highly homologous to that of mammalian EHDs.

AtEHDs, novel Arabidopsis EH-domain-containing proteins involved in endocytosis

SUMMARY

Endocytosis is an essential process by which the eukaryotic cell internalizes exogenous material. Studies in yeast and mammalian cells have revealed that endocytosis is a complex molecular process depending on regulated interactions between a variety of proteins and lipids through specific modules. One such module is the Eps15 homology (EH) domain, a conserved modular protein-interaction domain found in several endocytic proteins. The EH-domain-containing proteins function as regulators of endocytosis through their ability to interact with other proteins involved in this process. Here we describe the isolation and characterization of two Arabidopsis EH-domain-containing proteins (AtEHD1 and AtEHD2). We show that the two proteins are involved in endocytosis in plant systems and demonstrate that the Arabidopsis EHD proteins function similarly to mammalian EHDs. Similarly to hEHD2, over-expression of AtEHD2 has an inhibitory effect on endocytosis. While transgenic plants over-expressing AtEHD1 had no detectable phenotype, downregulation of AtEHD1 caused retardation of entry of endocytosed material into plant cells.

Impact of larviciding with a Bacillus thuringiensis israelensis formulation, VectoBac WG, on dengue mosquito vectors in a dengue endemic site in Selangor State, Malaysia

The field bioefficacy of a wettable granule (WG) formulation of Bacillus thuringiensis israelensis (Bti), VectoBac WG (Bti strain AM65-52) against dengue vectors, Aedes aegypti and Ae albopictus; was evaluated in a suburban residential area (TST) and in a temporary settlement site (KB) in the state of Selangor, Malaysia. Pre-control ovitrap surveillance of the trial sites indicated a high population of both types of Aedes mosquitoes. The populations were monitored continuously by weekly ovitrapping. Bti was sprayed biweekly at a dosage of 500 g/ha by using a mist-blower. The spray application was targeted into outdoor larval habitats. If required, Bti formulation was also applied directly into indoor water-holding containers at 8 g/1,000 l. Based on ovitrap surveillance, a significant reduction in Aedes populations was evident 4 weeks after initiating the first Bti treatment. The ovitrap index (OI) and the larvae density decreased drastically in both trial sites. In TST, the indoor OI was significantly reduced from 57.50 +/- 7.50% to 19.13 +/- 5.49% (p<0.05), while the outdoor OI decreased from 38.89 +/- 11.11% to 15.36 +/- 5.93%. In KB, similarly, the OI was significantly reduced by more than half, from 66.66 +/- 6.67% to 30.26 +/- 2.99% (p< 0.05). In all cases, the reduction in OI was paralleled by reduction in larval density.

Defective ubiquitinylation of EGFR mutants of lung cancer confers prolonged signaling

Several distinct mutations within the kinase domain of the epidermal growth factor receptor (EGFR) are associated with non-small cell lung cancer, but mechanisms underlying their oncogenic potential are incompletely understood. Although normally ligand-induced kinase activation targets EGFR to Cbl-mediated receptor ubiquitinylation and subsequent degradation in lysosomes, we report that certain EGFR mutants escape this regulation. Defective endocytosis characterizes a deletion mutant of EGFR, as well as a point mutant (L858R-EGFR), whose association with c-Cbl and ubiquitinylation are impaired. Our data raise the possibility that refractoriness of L858R-EGFR to downregulation is due to enhanced heterodimerization with the oncogene product HER2, which leads to persistent stimulation.

A systematic review of randomized controlled trials for plasma exchange in the treatment of thrombotic thrombocytopenic purpura

The mainstay of treatment for thrombotic thrombocytopenic purpura (TTP) is plasma exchange (PE). A systematic review was undertaken to summarize the randomized controlled trial (RCT) evidence, to date, on PE as treatment for TTP. Seven randomized RCTs were identified till May 2005. A statistical reduction in mortality was found in patients receiving PE compared with patients receiving plasma infusion (relative risk 0.31, 95% confidence interval 0.12-0.79). No statistical difference in mortality was found in trials comparing different replacement fluids for PE. There were few differences in the response to treatment and the resolution of the presenting signs of TTP in any trial. Lack of data prevented a full assessment of the incidence of adverse events. None of the studies included measured patients' quality of life. Further research is required to determine the benefits and side effects associated with different replacement fluids for PE. It is recommended that there should be consistency in the diagnostic criteria, measurement of clinical outcomes and length of follow up. Continued support of existing TTP patient registries and establishment of new registries would facilitate this.

The three-dimensional structure of complex I from Yarrowia lipolytica: a highly dynamic enzyme

The structure of complex I from Yarrowia lipolytica was determined by three-dimensional electron microscopy. A random conical data set was collected from deep stain embedded particles. More than 14000 image pairs were analyzed. Through extensive classification combined with three-dimensional reconstruction, it was possible for the first time to show a much more detailed substructure of the complex. The peripheral arm is subdivided in at least six domains. The membrane arm shows two major protrusions on its matrix facing side and exhibits a channel like feature on the side facing the cytoplasm. Structures resembling a tether connecting the subunits near the catalytic center with the protrusions of the membrane arm provide a second connection between matrix and membrane domain.

Long-term results of radiofrequency ablation of slow pathway in patients with atrioventricular nodal reentrant tachycardia: single-center experience

BACKGROUND

This study sought to evaluate the long-term recurrence rate of atrioventricular nodal reentrant tachycardia (AVNRT) after radiofrequency catheter ablation. The clinical and electrophysiological features of patients with AVNRT and their immediate outcomes after undergoing slow pathway ablation/modification were also studied.

METHODS AND RESULTS

The study included 264 consecutive patients with AVNRT (mean age 46 -/+ 15 years, 143 women, 121 men) who underwent slow pathway ablation/modification using a combined electrophysiological and anatomical approach. The primary endpoint of ablation procedure was non- inducibility of the arrhythmia. The primary endpoint of the study was the recurrence of AVNRT on follow-up. Acute success was achieved in 262 (99.6%) patients. Complication rate of the ablation procedure was 2.6% and the average fluoroscopy time was 18.3 -/+ 11 minutes. The patients were followed up for a mean duration of 20 -/+ 9 months during which there was only one case of recurrence.

CONCLUSION

Radiofrequency ablation or modification of slow pathway is highly effective in the treatment of AVNRT. The technique has a high initial success rate and a low complication rate. The recurrence rates are extremely low (0.3%) on long-term follow-up.

Survey of the use and clinical effectiveness of HPA-1a/5b-negative platelet concentrates in proven or suspected platelet alloimmunization

The optimal treatment of neonatal alloimmune thrombocytopenia (NAIT) is the transfusion of compatible donor platelets. The National Blood Service in England has established panels of "accredited" donors negative for human platelet antigens HPA-1a and HPA-5b, the most commonly implicated alloantigens. We have retrospectively surveyed the frequency of use and clinical effectiveness of donations collected over a 13-month period from the Oxford accredited panel. Ninety-five per cent of hyperconcentrated platelets (HPCs) collected were issued, all for intrauterine transfusion to fetuses at risk of NAIT due to the presence of maternal platelet alloantibodies and previously affected siblings. Thirty-one per cent of paediatric platelet concentrates (PPCs) collected were issued, of which 57% were used for cases of suspected NAIT. Fifty-four per cent of adult therapeutic doses collected were issued; 5% of these were used in cases of suspected NAIT or proven post-transfusion purpura (PTP). Good increments were seen in most NAIT cases transfused with HPCs or PPCs, and a moderate increment in the one PTP case. We conclude that the establishment of accredited panels is justified and enables delivery of a clinically effective treatment for NAIT. Increased use and cost-effectiveness could be achieved by the delivery of an educational programme to neonatal unit clinical staff to increase the awareness and appropriate treatment of NAIT.

EHD3: a protein that resides in recycling tubular and vesicular membrane structures and interacts with EHD1

Here we report the characterization of an eps15 homology (EH) domain containing protein designated EHD3. EHD3 was mapped to human chromosome 2p22-23, while the murine Ehd3 homolog was mapped to chromosome 17p21. Both the human and the mouse genes contain a polymorphic (CA) repeat in their 3'UTR. One 3.6-kb Ehd3 transcript was mainly detected in adult mouse brain and kidney and at day 7 of mouse development. On the other hand, human tissues exhibited two, 4.2- and 3.6-kb, EHD3 RNA species. They were predominantly expressed in heart, brain, placenta, liver, kidney and ovary. EHD3, expressed as a green fluorescent fusion protein was localized to endocytic vesicles and to microtubule-dependent, membrane tubules. There was a clear colocalization of EHD3-positive structures and transferrin-containing recycling vesicles, implying that EHD3 resides within the endocytic recycling compartment. Shuffling the N-terminal domain of EHD1 (previously shown to reside in the transferrin-containing, endocytic recycling compartment) with that of EHD3 resulted in a chimeric EHD protein that was localized mainly to tubules instead of the endocytic vesicles, implicating the N-terminal domain as responsible for the tubular localization of EHD3. Mutant EHD3 forms, missing the N-terminal or the C-terminal domains, lost their tubular localization. Results of two-hybrid analyses indicated that EHD1 and EHD3 interact with each other. In addition, EHD1 and EHD3 could be coimmunoprecipitated from cellular extracts, confirming the interaction implied by two-hybrid analysis. Moreover, coexpression of EHD1 and EHD3 resulted in their colocalization in microtubule-dependent tubules as well as in punctate forms. Based on its specific intracellular localization and its interaction with EHD1, we postulate that EHD3 localizes on endocytic tubular and vesicular structures and regulates their microtubule-dependent movement.

Associations between adverse events in childhood and chronic widespread pain in adulthood: are they explained by differential recall?

OBJECTIVE

Clinic based studies suggest that adverse events in childhood may predispose to chronic pain in adult life. These have been conducted on highly selected groups, and it is unknown whether these relationships hold in the general population and to what extent the increased rate of adverse childhood events in persons with pain is an artefact of differential reporting. We examined the hypothesis that chronic widespread pain was associated with reports of adverse experiences in childhood and whether any observed relationships could be explained by differential recall.

METHODS

A cross sectional population based screening survey was conducted. Subjects completed a questionnaire that included assessments of pain and psychological state. In total, 296 subjects who had demonstrated psychological distress were randomly selected and had a detailed interview, which included an assessment of 14 adverse childhood experiences. Medical records relating to childhood were also examined for those subjects.

RESULTS

The prevalence of self-reported adverse childhood experiences was greatest in adult subjects with current chronic widespread pain. Exposure to illness in family members, parental loss, operations, and abuse were all associated with increased, but nonsignificant, odds of having chronic widespread pain versus those without such exposures. However the only statistically significant association was with childhood hospitalizations. From medical record information the associations of hospitalizations (OR 5.1, 95% CI 2.0-13.0) and operations (OR 3.0, 95% CI 1.2-7.2) with pain previously noted were partly explained by differential recall between subjects with and without pain: hospitalizations, OR 2.2, 95% CI 0.9-5.5; operations, OR 1.2, 95% CI 0.5-3.4.

CONCLUSION

Although several reported adverse events in childhood were observed to be associated with chronic widespread pain in adulthood, only reports of hospitalizations were significantly associated. Validation of self-reported exposures suggests that there was differential recall of past events among those with and without pain, and this differential recall explained the association between hospitalizations and current chronic pain. Such differential recall may explain other observations of an association between reports of adverse childhood events and chronic pain in adulthood.

A case ascertainment study of septic discitis: clinical, microbiological and radiological features

We studied the spectrum of septic discitis presenting to two busy district general hospitals over 2.5 years (November 1996 to April 1999), surveying the case notes of all patients attending Royal Bournemouth and Poole Hospitals with probable septic discitis on magnetic resonance imaging (MRI). Twenty-two cases of septic discitis were identified, suggesting an annual incidence of 2/100 000/year. Seventy-three percent of patients were aged > or =65 years. In 91% of patients, back pain was the presenting symptom, with neurological signs evident in 45% of patients. Fever >37.5 degrees C was present in 68% of patients, and a marked elevation of erythrocyte sedimentation rate (ESR) in 91%. Diagnosis was originally by MRI in 86% of patients, with plain radiographs not diagnostic of discitis in the early stages of the infection. Staphylococcus aureus was the commonest pathogen (41%), but in 18% of patients, no organism was identified. The major predisposing factors to septic discitis were invasive procedures (41%), underlying cancer (25%) and diabetes (18%). Pre-existing degenerative spinal disease was found in 50% of patients. Four patients whose causative organism was not isolated had a poorer outcome: one death and three with increased morbidity. Our estimated incidence rate (2/100 000/year) is higher than that in previous studies and may be due to a higher detection rate with MRI and/or a genuine increase in the number of cases. Septic discitis should be considered in any patient who has severe localized pain at any spinal level, especially if accompanied by fever and elevated ESR, or in the immunosuppressed.

Features of somatization predict the onset of chronic widespread pain: results of a large population-based study

OBJECTIVE

Chronic widespread pain, the clinical hallmark of the fibromyalgia syndrome, is associated with other physical and psychological symptoms both in patients studied in a clinical setting and in those identified in the community. The present study was undertaken to examine the hypothesis that psychological and physical indicators of the process of somatization predict the development of new chronic widespread pain.

METHODS

In this population-based prospective study, 1,658 adults ages 18-65 years completed a detailed pain questionnaire, which included a pain drawing. They also completed the following psychosocial instruments: General Health Questionnaire, Somatic Symptom Checklist, Fatigue Questionnaire, and Illness Attitude Scales. Individuals were followed up at 12 months, at which time 1,480 (93% of subjects still living at their baseline address) provided data on pain status, using the same instruments.

RESULTS

At baseline, 825 subjects were classified as pain free and 833 as having pain not satisfying criteria for chronic widespread pain. Of those, 18 (2%) and 63 (8%), respectively, were classified as having chronic widespread pain at followup. After adjustment for age and sex, there were strong relationships between baseline test scores and subsequent risk of chronic widespread pain (odds ratio for the Somatic Symptom Checklist 3.3; odds ratio for the Illness Behavior subscale of the Illness Attitude Scales 9.0). All 95% confidence intervals excluded unity. These associations were independent of baseline pain status.

CONCLUSION

Subjects who are free of chronic widespread pain are at increased future risk of its development if they display other aspects of the process of somatization. Data from this population-based prospective study lend powerful support to the hypothesis that chronic widespread pain can be one manifestation of the somatization of distress.

A quality approach for conducting training needs assessments in the Ministry of Health, State of Bahrain

In health care organizations around the world, Training Needs Assessments (TNAs) have generally followed a professions-based approach. For example, the training needs of doctors, nurses, each allied health profession, and distinct support staff have been analyzed separately--individualized TNAs conducted for each speciality and functional area. Although a professions-based TNA model can provide useful information to human resource development (HRD) professionals, there are two major drawbacks: (1) it is possible that important training needs might be overlooked because of lack of information sharing among professions and (2) such an approach does not encourage an interdisciplinary, team orientation to service provision. This paper proposes an improved method of conceptualizing TNAs, using an approach that builds on the quality management literature (TQM, CQI, etc.) which stresses the importance of customer- and service-orientations to organizing and measuring organizational and individual performance.

Disability and mental health of patients waiting for total hip replacement

We performed a cross sectional study to examine the relationship between physical function and mental health of patients waiting for total hip replacement surgery, and the relationship between physical and social function and mental health to time spent waiting for surgery. We found that, in addition to the expected poor hip function, limited mobility and pain, one-quarter of the patients had clinically significant mood disorders and another quarter were in the borderline range. No association was found between severity of mental disorder and assessment of hip function. The patients had been waiting for 1-26 months (median 6 months) for surgery: yet those waiting longest were no worse on any of the outcome measures and their mental health was better. We conclude that mental disorders are common in patients waiting for hip replacements, are not directly related to hip function and their origins are unknown, but they require clinical assessment and treatment. There is no evidence that physical or social function or mental health are worse in those waiting longer for hip replacement surgery. Even so, these patients are severely disabled and some have to wait too long.

Effect of light/dark regimen on N-nitrosoethylurea-induced transplacental carcinogenesis in rats

Pregnant females were randomly subdivided into three groups (24 rats per group) and kept at the 12:12 h light/dark regimen (group 1), at the constant light illumination (24 h a day, group 2) or at the continuous darkness (group 3). N-nitrosoethylurea (NEU) has been injected into the tail vein of all rats (80 mg/kg) on the 18-19th day of the pregnancy. After the delivery the lacting dams and their progeny during the lactation period (1 month after delivery) were kept also at the three different light/dark regimens. Then all offspring from each group was kept at the 12:12 h light/dark regimen, males and females separately, and were observed until natural death. The exposure to constant light significantly promoted the transplacental carcinogenesis whereas the exposure to constant darkness inhibited it. The incidence of total tumors, tumors of both a peripheral nervous system and kidney was 2.6; 2.5 and 8.5 times higher, and survival significantly shorter, correspondingly, in rats from the group 2 exposed to the constant light regimen as compared to the group 1 (12:12 h light/dark regimen) (P<0.05). On the other hand, the exposure to the continuous darkness during the pregnancy and the lactation period significantly inhibited the transplacental carcinogenesis in the offspring of rats treated with NEU. The incidence of total tumors, tumors of a peripheral nervous system was by 2.4 and 2.7 times less, and survival longer, respectively, in exposed to the darkness rats from the group 3 as compared to the group 1 (12:12 h light/dark regimen) (P<0.05). Thus, our data firstly have shown the modifying effect of light-dark regimen on the realization of the transplacental carcinogenesis induced by NEU in rats.

Application of "VITALS": visual indicators of teaching and learning success in reporting student evaluations of clinical teachers

CONTEXT

At the College of Medicine and Medical Sciences, Arabian Gulf University, Bahrain, a system has been introduced in which clerkship students evaluate clinical faculty using Visual Indicators of Teaching and Learning Success (VITALS).

OBJECTIVE

To describe the use of VITALS in reporting student feedback on teaching and learning effectiveness of clinical faculty in the clerkship.

DESIGN

Descriptive study.

SUBJECTS

A total of 210 clerkship students evaluated 76 clinical tutors over a period of 3 years. Feedback was also obtained from seven programme managers and one supportive staff member.

METHOD

Nine indicators of effective clinical teaching were identified through a literature search. Students individually reported on clinical faculty teaching capabilities using a 5-point, Likert-type scale. Cumulative reports of students' feedback on clinical faculty teaching were prepared using opposing bar graphs, reflecting perceived areas of strength or weakness in each teacher's performance.

RESULTS

A total of 1450 evaluation forms were completed by 180 of 210 students (85.7%). VITALS graph representations of students' perceptions of clinical tutors were communicated to each clinical tutor at the end of each clerkship and academic year. Twenty-one students out of 53 who gave written comments were related to VITALS. They reflected a positive view of VITALS as a process or tool of faculty evaluation. Clinical faculty (18), programme managers(7) and supporting staff (1) gave comments indicating acceptance of the system.

CONCLUSION

This preliminary study suggests that VITALS could be an effective tool for improving clinical teaching. It is acceptable to students, faculty and managers of educational programmes. The database reflecting their teaching and educational profiles were used to provide clinical faculty with constructive feedback.