Quench dynamics of edge states in a finite extended Su-Schrieffer-Heeger system

We examine the quench dynamics of an extended Su-Schrieffer-Heeger (SSH) model involving long-range hopping that can hold multiple topological phases. Using winding number diagrams to characterize the system's topological phases geometrically, it is shown that there can be multiple winding number transition paths for a quench between two topological phases. The dependence of the quench dynamics is studied in terms of the survival probability of the fermionic edge modes and postquench transport. For two quench paths between two topological regimes with the same initial and final topological phase, the survival probability of edge states is shown to be strongly dependent on the winding number transition path. This dependence is explained using energy band diagrams corresponding to the paths. Following this, the effect of the winding number transition path on transport is investigated. We find that the velocities of maximum transport channels varied along the winding number transition path. This variation depends on the path we choose, i.e., it increases or decreases depending upon the path. An analysis of the coefficient maps, energy spectrum, and spatial structure of the edge states of the final quench Hamiltonian provides an understanding of the path-dependent velocity variation phenomenon.

Host, environment, and anthropogenic factors drive landscape dynamics of an environmentally transmitted pathogen: Sarcoptic mange in the bare-nosed wombat

Understanding the spatial dynamics and drivers of wildlife pathogens is constrained by sampling logistics, with implications for advancing the field of landscape epidemiology and targeted allocation of management resources. However, visually apparent wildlife diseases, when combined with remote-surveillance and distribution modelling technologies, present an opportunity to overcome this landscape-scale problem. Here, we investigated dynamics and drivers of landscape-scale wildlife disease, using clinical signs of sarcoptic mange (caused by Sarcoptes scabiei) in its bare-nosed wombat (BNW; Vombatus ursinus) host. We used 53,089 camera-trap observations from over 3261 locations across the 68,401 km2 area of Tasmania, Australia, combined with landscape data and ensemble species distribution modelling (SDM). We investigated: (1) landscape variables predicted to drive habitat suitability of the host; (2) host and landscape variables associated with clinical signs of disease in the host; and (3) predicted locations and environmental conditions at greatest risk of disease occurrence, including some Bass Strait islands where BNW translocations are proposed. We showed that the Tasmanian landscape, and ecosystems therein, are nearly ubiquitously suited to BNWs. Only high mean annual precipitation reduced habitat suitability for the host. In contrast, clinical signs of sarcoptic mange disease in BNWs were widespread, but heterogeneously distributed across the landscape. Mange (which is environmentally transmitted in BNWs) was most likely to be observed in areas of increased host habitat suitability, lower annual precipitation, near sources of freshwater and where topographic roughness was minimal (e.g. human modified landscapes, such as farmland and intensive land-use areas, shrub and grass lands). Thus, a confluence of host, environmental and anthropogenic variables appear to influence the risk of environmental transmission of S. scabiei. We identified that the Bass Strait Islands are highly suitable for BNWs and predicted a mix of high and low suitability for the pathogen. This study is the largest spatial assessment of sarcoptic mange in any host species, and advances understanding of the landscape epidemiology of environmentally transmitted S. scabiei. This research illustrates how host-pathogen co-suitability can be useful for allocating management resources in the landscape.

Neoadjuvant therapy impact in early pancreatic cancer: "bioborderline" vs. "non-bioborderline"

Backgrounds/Aims

To analyze the results of the neoadjuvant treatment of patients in our center with early pancreatic cancer.

Methods

Eighty-four patients with early pancreatic cancer (I-II) were included, of which 59 were considered "bioborderline" (carbohydrate antigen [CA] 19-9 > 37 U/L), and 25 were considered "non-bioborderline" (CA19-9 < 37 U/L). The R0 resection rate, presence of negative nodes, survival, and recurrence rates were analyzed in two groups, the NEO group (neoadjuvant + surgery) and the non-NEO group (upfront surgery).

Results

A 28.6% pathologic complete response was observed in the NEO group of the whole sample. The residual R0 was 85.7%, and nodes were negative in 78.6% of the patients in the NEO group of bioborderline patients. All non-bioborderline patients treated with neoadjuvant were R0, and no affected nodes were observed in any of them. The median overall survival (OS) in patients with elevated CA19-9 levels in the NEO group was 31.4 months vs. 13.1 months in the non-NEO (log-rank test p = 0.006), with a 62% relative reduction in the mortality rate (hazard ratio = 0.38, 95% confidence interval: 0.20-0.79; p = 0.008). The median OS in patients with normal CA19-9 levels in the NEO group was 65.9 months vs. 16.2 months in the non-NEO group, without statistically significant differences between the two but with a trend toward significance (log-rank test p = 0.08).

Conclusions

A neoadjuvant strategy seemed to improve local control and the survival of patients with early pancreatic cancer, both those with elevated CA19-9 and normal marker levels.

Cancer and breast cancer awareness interventions in an intellectual disability context: A review of the literature

BACKGROUND

Women with an intellectual disability (ID) have a similar risk of developing breast cancer as women in the general population yet present with later stage breast cancers, which have poorer outcomes.

AIM

To identify whether there is a need to develop a breast cancer awareness intervention for women with an ID.

METHODS

Interventions aimed at increasing cancer awareness and breast cancer awareness for people with an ID were identified and critically appraised.

RESULTS

Five interventions to increase cancer awareness or breast cancer awareness in people with an ID were identified.

CONCLUSION

The review highlighted the paucity of theoretically underpinned breast cancer awareness interventions specifically aimed at women with an ID. Facilitating breast cancer awareness for women with an ID could potentially lead to earlier presentation of potential symptoms of breast cancer, earlier treatment, better prognosis and ultimately, improved survival. This article establishes that there is a need for an intervention underpinned by theory to increase breast cancer awareness in women with an ID.

Observation of a Quantum Phase from Classical Rotation of a Single Spin

The theory of angular momentum connects physical rotations and quantum spins together at a fundamental level. Physical rotation of a quantum system will therefore affect fundamental quantum operations, such as spin rotations in projective Hilbert space, but these effects are subtle and experimentally challenging to observe due to the fragility of quantum coherence. We report on a measurement of a single-electron-spin phase shift arising directly from physical rotation, without transduction through magnetic fields or ancillary spins. This phase shift is observed by measuring the phase difference between a microwave driving field and a rotating two-level electron spin system, and it can accumulate nonlinearly in time. We detect the nonlinear phase using spin-echo interferometry of a single nitrogen-vacancy qubit in a diamond rotating at 200 000 rpm. Our measurements demonstrate the fundamental connections between spin, physical rotation, and quantum phase, and they will be applicable in schemes where the rotational degree of freedom of a quantum system is not fixed, such as spin-based rotation sensors and trapped nanoparticles containing spins.

Instability of Rotationally Tuned Dipolar Bose-Einstein Condensates

The possibility of effectively inverting the sign of the dipole-dipole interaction, by fast rotation of the dipole polarization, is examined within a harmonically trapped dipolar Bose-Einstein condensate. Our analysis is based on the stationary states in the Thomas-Fermi limit, in the corotating frame, as well as direct numerical simulations in the Thomas-Fermi regime, explicitly accounting for the rotating polarization. The condensate is found to be inherently unstable due to the dynamical instability of collective modes. This ultimately prevents the realization of robust and long-lived rotationally tuned states. Our findings have major implications for experimentally accessing this regime.

Phase I/II Trial to Evaluate the Efficacy and Safety of Nanoparticle Albumin-Bound Paclitaxel in Combination With Gemcitabine in Patients With Pancreatic Cancer and an ECOG Performance Status of 2

Purpose

Gemcitabine plus nanoparticle albumin-bound (NAB) paclitaxel (GA) significantly improved survival compared with gemcitabine alone in patients with metastatic pancreatic ductal adenocarcinoma (PDAC) and a Karnofsky performance status (PS) of 70% or greater. Because of the low number of patients with reduced PS, the efficacy of this regimen in fragile patients remains unclear. This study aimed to evaluate the efficacy and tolerability of different GA dosing regimens in patients with a poor PS.

Patients and Methods

In the phase I part of this study, patients were randomly assigned to one of the following four parallel GA treatment arms (six patients per arm): a biweekly schedule of NAB-paclitaxel (150 mg/m2 [arm A] or 125 mg/m2 [arm C]) plus gemcitabine 1,000 mg/m2 or a standard schedule of 3 weeks on and 1 week off of NAB-paclitaxel (100 mg/m2 [arm B] or 125 mg/m2 [arm D]) plus gemcitabine 1,000 mg/m2. The two regimens with the better tolerability profile on the basis of predefined criteria were evaluated in the phase II part of the study, the primary end point of which was 6-month actuarial survival.

Results

Arms B and D were selected for the phase II part of the study. A total of 221 patients (111 patients in arm B and 110 patients in arm D) were enrolled. Baseline characteristics including median age (71 and 68 years in arms B and D, respectively), sex (51% and 55% men in arms B and D, respectively), and metastatic disease (88% and 84% in arms B and D, respectively) were comparable between arms. The most frequent grade 3 or 4 toxicities in arms B and D were anemia (12% and 7%, respectively), neutropenia (32% and 30%, respectively), thrombocytopenia (7% and 11%, respectively), asthenia (14% and 16%, respectively), and neurotoxicity (11% and 16%, respectively). In arms B and D, there were no significant differences in response rate (24% and 28%, respectively), median progression-free survival (5.7 and 6.7 months, respectively), and 6-month overall survival (63% and 69%, respectively).

Conclusion

NAB-paclitaxel administered at either 100 and 125 mg/m2 in combination with gemcitabine on days 1, 8, and 15 every 28 days is well tolerated and results in acceptable safety and efficacy in patients with metastatic pancreatic ductal adenocarcinoma and a poor PS.

Conservation of rare and local breeds of livestock

The genetic diversity of domesticated species is contained within breeds, with the result that conserving breeds conserves this diversity. Breeds are predictable genetic resources that allow a match of animals with different environments and production goals. Breeds were developed through a process involving foundation, isolation and selection. Breed types that qualify as genetic resources include 'landraces' (local breeds), standardised breeds, commercial production breeds and feral livestock that have returned to a free-living state. Currently, breeds of all classes are threatened with extinction. The reasons for breed conservation include maintaining breed diversity for future needs, cultural connections between people and breeds, and material for scientific investigation. Several breeds have undergone genetic adaptations that make them uniquely suited to specific challenging environments. Conservation depends upon discovering these genetic resources, securing them with a good genetic structure, and subsequently sustaining them for long-term survival with demand for the breed and its products.

The nutrient-sensing repertoires of mouse enterochromaffin cells differ between duodenum and colon

BACKGROUND

Enterochromaffin (EC) cells within the gastrointestinal (GI) tract provide almost all body serotonin (5-hydroxytryptamine [5-HT]). Peripheral 5-HT, released from EC cells lining the gut wall, serves diverse physiological roles. These include modulating GI motility, bone formation, hepatic gluconeogenesis, thermogenesis, insulin resistance, and regulation of fat mass. Enterochromaffin cells are nutrient sensors, but which nutrients they are responsive to and how this changes in different parts of the GI tract are poorly understood.

METHODS

To accurately undertake such an examination, we undertook the first isolation and purification of primary mouse EC cells from both the duodenum and colon in the same animal. This allowed us to compare, in an internally controlled manner, regional differences in the expression of nutrient sensors in EC cells using real-time PCR.

KEY RESULTS

Both colonic and duodenal EC cells expressed G protein-coupled receptors and facilitative transporters for sugars, free fatty acids, amino acids, and lipid amides. We find differential expression of nutrient receptor and transporters in EC cells obtained from duodenal and colonic EC cells. Duodenal EC cells have higher expression of tryptophan hydroxylase-1, sugar transporters GLUT2, GLUT5, and free fatty acid receptors 1 and 3 (FFAR1 and FFAR3). Colonic EC cells express higher levels of GLUT1, FFAR2, and FFAR4.

CONCLUSIONS & INFERENCES

We highlight the diversity of EC cell physiology and identify differences in the regional sensing repertoire of EC cells to an assortment of nutrients. These data indicate that not all EC cells are similar and that differences in their physiological responses are likely dependent on their location within the GI tract.

Vortices and vortex lattices in quantum ferrofluids

The experimental realization of quantum-degenerate Bose gases made of atoms with sizeable magnetic dipole moments has created a new type of fluid, known as a quantum ferrofluid, which combines the extraordinary properties of superfluidity and ferrofluidity. A hallmark of superfluids is that they are constrained to rotate through vortices with quantized circulation. In quantum ferrofluids the long-range dipolar interactions add new ingredients by inducing magnetostriction and instabilities, and also affect the structural properties of vortices and vortex lattices. Here we give a review of the theory of vortices in dipolar Bose-Einstein condensates, exploring the interplay of magnetism with vorticity and contrasting this with the established behaviour in non-dipolar condensates. We cover single vortex solutions, including structure, energy and stability, vortex pairs, including interactions and dynamics, and also vortex lattices. Our discussion is founded on the mean-field theory provided by the dipolar Gross-Pitaevskii equation, ranging from analytic treatments based on the Thomas-Fermi (hydrodynamic) and variational approaches to full numerical simulations. Routes for generating vortices in dipolar condensates are discussed, with particular attention paid to rotating condensates, where surface instabilities drive the nucleation of vortices, and lead to the emergence of rich and varied vortex lattice structures. We also present an outlook, including potential extensions to degenerate Fermi gases, quantum Hall physics, toroidal systems and the Berezinskii-Kosterlitz-Thouless transition.

Persistent Superfluid Flow Arising from the He-McKellar-Wilkens Effect in Molecular Dipolar Condensates

We show that the He-McKellar-Wilkens effect can induce a persistent flow in a Bose-Einstein condensate of polar molecules confined in a toroidal trap, with the dipolar interaction mediated via an electric dipole moment. For Bose-Einstein condensates of atoms with a magnetic dipole moment, we show that although it is theoretically possible to induce persistent flow via the Aharonov-Casher effect, the strength of the electric field required is prohibitive. We also outline an experimental geometry tailored specifically for observing the He-McKellar-Wilkens effect in toroidally trapped condensates.

Demographic drivers of age-dependent sexual selection

Sexual selection has a critical role in evolution, and it is fundamental to identify what ecological factors drive its variation. Disentangling the ecological correlates of sexual selection over the long term, however, is challenging and has rarely been done in nature. We sought to assess how demographic changes influenced the intensity, direction and form of sexual selection and whether selective pressures varied with age. We tested whether breeder sex ratio, number of competitors and age structure influenced selection differentials on horn length of wild bighorn rams (Ovis canadensis) of different age classes on Ram Mountain, Alberta. We used 21 years of data including a detailed pedigree, demographic parameters and repeated morphological measurements. Sexual selection on horn length of males of all ages was directional and positive. Selection intensity increased with the number of competitors, reflecting male-male encounter rate during the rut, but was independent of breeder sex ratio or age structure. This result can also be linked to changes in population size because the number of competitors was highly correlated to total number of sheep. This demographic effect likely arises from age-dependent mating tactics. Males aged 2-4 years are weakly competitive and experienced stronger sexual selection as they accounted for a greater proportion of all males. Selection experienced by mature males appeared independent of demography. Our study provides a rare description of the demographic determinants of sexual selection in nature.

Paucity of PD-L1 expression in prostate cancer: innate and adaptive immune resistance

BACKGROUND

Primary prostate cancers are infiltrated with programmed death-1 (PD-1) expressing CD8+ T-cells. However, in early clinical trials, men with metastatic castrate-resistant prostate cancer did not respond to PD-1 blockade as a monotherapy. One explanation for this unresponsiveness could be that prostate tumors generally do not express programmed death ligand-1 (PD-L1), the primary ligand for PD-1. However, lack of PD-L1 expression in prostate cancer would be surprising, given that phosphatase and tensin homolog (PTEN) loss is relatively common in prostate cancer and several studies have shown that PTEN loss correlates with PD-L1 upregulation--constituting a mechanism of innate immune resistance. This study tested whether prostate cancer cells were capable of expressing PD-L1, and whether the rare PD-L1 expression that occurs in human specimens correlates with PTEN loss.

METHODS

Human prostate cancer cell lines were evaluated for PD-L1 expression and loss of PTEN by flow cytometry and western blotting, respectively. Immunohistochemical (IHC) staining for PTEN was correlated with PD-L1 IHC using a series of resected human prostate cancer samples.

RESULTS

In vitro, many prostate cancer cell lines upregulated PD-L1 expression in response to inflammatory cytokines, consistent with adaptive immune resistance. In these cell lines, no association between PTEN loss and PD-L1 expression was apparent. In primary prostate tumors, PD-L1 expression was rare, and was not associated with PTEN loss.

CONCLUSIONS

These studies show that some prostate cancer cell lines are capable of expressing PD-L1. However, in human prostate cancer, PTEN loss is not associated with PD-L1 expression, arguing against innate immune resistance as a mechanism that mitigates antitumor immune responses in this disease.

Comparing measures of breeding inequality and opportunity for selection with sexual selection on a quantitative character in bighorn rams

The reliability and consistency of the many measures proposed to quantify sexual selection have been questioned for decades. Realized selection on quantitative characters measured by the selection differential i was approximated by metrics based on variance in breeding success, using either the opportunity for sexual selection Is or indices of inequality. There is no consensus about which metric best approximates realized selection on sexual characters. Recently, the opportunity for selection on character mean OSM was proposed to quantify the maximum potential selection on characters. Using 21 years of data on bighorn sheep (Ovis canadensis), we investigated the correlations between seven indices of inequality, Is , OSM and i on horn length of males. Bighorn sheep are ideal for this comparison because they are highly polygynous and sexually dimorphic, ram horn length is under strong sexual selection, and we have detailed knowledge of individual breeding success. Different metrics provided conflicting information, potentially leading to spurious conclusions about selection patterns. Iδ, an index of breeding inequality, and, to a lesser extent, Is showed the highest correlation with i on horn length, suggesting that these indices document breeding inequality in a selection context. OSM on horn length was strongly correlated with i, Is and indices of inequality. By integrating information on both realized sexual selection and breeding inequality, OSM appeared to be the best proxy of sexual selection and may be best suited to explore its ecological bases.

Anisotropic and long-range vortex interactions in two-dimensional dipolar Bose gases

We perform a theoretical study into how dipole-dipole interactions modify the properties of superfluid vortices within the context of a two-dimensional atomic Bose gas of co-oriented dipoles. The reduced density at a vortex acts like a giant antidipole, changing the density profile and generating an effective dipolar potential centred at the vortex core whose most slowly decaying terms go as 1/ρ(2) and ln(ρ)/ρ(3). These effects modify the vortex-vortex interaction which, in particular, becomes anisotropic for dipoles polarized in the plane. Striking modifications to vortex-vortex dynamics are demonstrated, i.e., anisotropic corotation dynamics and the suppression of vortex annihilation.

Fetal cardiac function in recipient twins undergoing fetoscopic laser ablation of placental anastomoses for Stage IV twin-twin transfusion syndrome

OBJECTIVE

Cardiac dysfunction is common in the recipient fetus of twin-twin transfusion syndrome (TTTS). In this study, we aimed to document the severity of fetal cardiac dysfunction in Stage IV TTTS (fetal hydrops) and assess evolution of cardiac function longitudinally after fetoscopic laser surgery.

METHODS

We reviewed obstetric ultrasound examination data, pre- and postoperative echocardiograms and neonatal outcomes for 22 cases of Stage IV TTTS undergoing fetoscopic laser ablation of placental anastomoses between 1998 and 2011. Myocardial performance index, atrioventricular valve flow patterns, ventricular shortening fraction, ventricular hypertrophy, outflow tract obstruction and venous Doppler waveforms were assessed.

RESULTS

Nineteen fetuses (86.4%) had ascites, eight (36.4%) had pleural effusions, nine (40.9%) had a pericardial effusion and 12 (54.5%) had subcutaneous edema at presentation. Preoperatively, cardiac function was grossly abnormal in all. Eight fetuses (36.4%) had functional pulmonary atresia and one (4.5%) had functional aortic atresia. Seventy-seven percent of recipient fetuses survived until birth. Postoperative echocardiographic follow-up (mean, 26 days) showed that indices of fetal cardiac function improved considerably, but never completely normalized. Six of the eight fetuses with functional pulmonary atresia (75.0%), as well as the fetus with functional aortic atresia, survived to birth. In all cases, the functional atresia resolved within 48 h of laser ablation therapy and none had structural valve anomalies at birth. All fetal effusions resolved after the laser.

CONCLUSIONS

Fetoscopic laser ablation of placental anastomoses reverses cardiac dysfunction and valvulopathy, even in the most severe cases of TTTS. However, recovery takes longer than in early stage disease.

Bevacizumab in Combination with Capecitabine plus Irinotecan as First-Line Therapy in Metastatic Colorectal Cancer: A Pooled Analysis of 2 Phase II Trials

BACKGROUND

Although phase III studies have investigated the effect of adding bevacizumab to the 3-weekly capecitabine plus irinotecan (XELIRI) combination in the first-line treatment of metastatic colorectal cancer (mCRC), no phase III studies investigating the effects of adding bevacizumab to biweekly XELIRI have been published.

PATIENTS AND METHODS

A retrospective pooled analysis of 2 single-arm phase II studies was performed. Previously untreated patients with mCRC received irinotecan 175 mg/m(2) on day 1 followed by capecitabine 1,000 mg/m(2) twice daily on days 2-8 every 2 weeks with or without bevacizumab 5 mg/kg on day 1.

RESULTS

In total, 53 patients received XELIRI, and 46 patients received XELIRI plus bevacizumab. There was a statistically significant increase in partial response rate with XELIRI plus bevacizumab (63 vs. 26% for XELIRI; p = 0.0002) and overall response rate (67 vs. 32%; p = 0.0005). Median time to disease progression was significantly longer with XELIRI plus bevacizumab (12.3 vs. 9.0 months for XELIRI; p = 0.012); median overall survival did not differ significantly between treatments (23.7 vs. 19.3 months; p = 0.4997). The proportion of patients experiencing at least 1 grade 3/4 adverse event was similar with both treatments (XELIRI, 47%; XELIRI plus bevacizumab, 44%).

CONCLUSION

This retrospective pooled analysis suggests that XELIRI plus bevacizumab has an acceptable tolerability profile and improves efficacy outcomes compared with XELIRI in the first-line treatment of mCRC.

Measurable quantum geometric phase from a rotating single spin

We demonstrate that the internal magnetic states of a single nitrogen-vacancy defect, within a rotating diamond crystal, acquire geometric phases. The geometric phase shift is manifest as a relative phase between components of a superposition of magnetic substates. We demonstrate that under reasonable experimental conditions a phase shift of up to four radians could be measured. Such a measurement of the accumulation of a geometric phase, due to macroscopic rotation, would be the first for a single atom-scale quantum system.

Numerical method for evolving the dipolar projected Gross-Pitaevskii equation

We describe a method for evolving the projected Gross-Pitaevskii equation (PGPE) for an interacting Bose gas in a harmonic-oscillator potential, with the inclusion of a long-range dipolar interaction. The central difficulty in solving this equation is the requirement that the field is restricted to a small set of prescribed modes that constitute the low-energy c -field region of the system. We present a scheme, using a Hermite-polynomial-based spectral representation, which precisely implements this mode restriction and allows an efficient and accurate solution of the dipolar PGPE. We introduce a set of auxiliary oscillator states to perform a Fourier transform necessary to evaluate the dipolar interaction in reciprocal space. We extensively characterize the accuracy of our approach and derive Ehrenfest equations for the evolution of the angular momentum.

The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils

Global climate change has accelerated the pace of glacial retreat in high-latitude and high-elevation environments, exposing lands that remain devoid of vegetation for many years. The exposure of 'new' soil is particularly apparent at high elevations (5000 metres above sea level) in the Peruvian Andes, where extreme environmental conditions hinder plant colonization. Nonetheless, these seemingly barren soils contain a diverse microbial community; yet the biogeochemical role of micro-organisms at these extreme elevations remains unknown. Using biogeochemical and molecular techniques, we investigated the biological community structure and ecosystem functioning of the pre-plant stages of primary succession in soils along a high-Andean chronosequence. We found that recently glaciated soils were colonized by a diverse community of cyanobacteria during the first 4-5 years following glacial retreat. This significant increase in cyanobacterial diversity corresponded with equally dramatic increases in soil stability, heterotrophic microbial biomass, soil enzyme activity and the presence and abundance of photosynthetic and photoprotective pigments. Furthermore, we found that soil nitrogen-fixation rates increased almost two orders of magnitude during the first 4-5 years of succession, many years before the establishment of mosses, lichens or vascular plants. Carbon analyses (pyrolysis-gas chromatography/mass spectroscopy) of soil organic matter suggested that soil carbon along the chronosequence was of microbial origin. This indicates that inputs of nutrients and organic matter during early ecosystem development at these sites are dominated by microbial carbon and nitrogen fixation. Overall, our results indicate that photosynthetic and nitrogen-fixing bacteria play important roles in acquiring nutrients and facilitating ecological succession in soils near some of the highest elevation receding glaciers on the Earth.

Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil

Soil microbial communities have the metabolic and genetic capability to adapt to changing environmental conditions on very short time scales. In this paper we combine biogeochemical and molecular approaches to reveal this potential, showing that microbial biomass can turn over on time scales of days to months in soil, resulting in a succession of microbial communities over the course of a year. This new understanding of the year-round turnover and succession of microbial communities allows us for the first time to propose a temporally explicit N cycle that provides mechanistic hypotheses to explain both the loss and retention of dissolved organic N (DON) and inorganic N (DIN) throughout the year in terrestrial ecosystems. In addition, our results strongly support the hypothesis that turnover of the microbial community is the largest source of DON and DIN for plant uptake during the plant growing season. While this model of microbial biogeochemistry is derived from observed dynamics in the alpine, we present several examples from other ecosystems to indicate that the general ideas of biogeochemical fluxes being linked to turnover and succession of microbial communities are applicable to a wide range of terrestrial ecosystems.

Dynamical instability of a rotating dipolar Bose-Einstein condensate

We analyze the hydrodynamic solutions for a dilute Bose-Einstein condensate with long-range dipolar interactions in a rotating, elliptical harmonic trap. The static solutions and their regimes of dynamical instability vary nontrivially with the strength of the dipolar interactions. We comprehensively map out this behavior, and, in particular, examine the experimental routes toward unstable dynamics, which, in analogy to conventional condensates, may lead to vortex lattice formation.

HLA-B*5701 typing by sequence-specific amplification: validation and comparison with sequence-based typing

Susceptibility to abacavir hypersensitivity (ABC HSR) is strongly associated with alleles carried on the 57.1 ancestral haplotype including HLA-B*5701 and Hsp70 Hom M493T. In one study, prospective testing for HLA-B*5701 and exclusion of individuals carrying this allele, from receiving abacavir, substantially lowered the incidence of ABC HSR to 0% (95% confidence interval 0-0.075%). The presence of HLA-B*5701 is usually detected by standard serological tests and by molecular genetic methods such as sequence-based typing (SBT). While the former test cannot discriminate between HLA-B57 subtypes, the expensive SBT may not be readily available in all laboratories. Hence, an alternate method was developed to detect HLA-B*5701 using allele and group-specific polymerase chain reaction-sequence-specific primers (PCR-SSP) typing. This PCR-SSP-typing method positively amplified all HLA-B*5701 alleles in concordance with their SBT-assigned typing. This multiplexed SSP assay was able to distinguish between HLA-B*5701 (n = 10) and closely related HLA-B57 alleles B*5702 (n = 2), -B*5703 (n = 1), -B*5704 (n = 1) alleles and non-HLA-B*57 alleles (n = 61). In conclusion, this method of HLA-B*5701 detection is a rapid and accurate typing method with high specificity, sensitivity and reproducibility.

Anomalous quantum reflection of Bose-Einstein condensates from a silicon surface: the role of dynamical excitations

We investigate the effect of interatomic interactions on the quantum-mechanical reflection of Bose-Einstein condensates from regions of rapid potential variation. The reflection process depends critically on the density and incident velocity of the condensate. For low densities and high velocities, the atom cloud has almost the same form before and after reflection. Conversely, at high densities and low velocities, the reflection process generates solitons and vortex rings that fragment the condensate. We show that this fragmentation can explain the anomalously low reflection probabilities recently measured for low-velocity condensates incident on a silicon surface.

Absence of BRAF mutations in UV-protected mucosal melanomas

BACKGROUND

Mutations in BRAF have recently been identified in a significant percentage of primary and metastatic cutaneous malignant melanomas. As ultraviolet (UV) exposure may play a role in the development of cutaneous melanoma lesions with BRAF mutations, BRAF mutation frequency in melanomas arising in sites protected from sun exposure may be lower than those from sun-exposed areas. Thus, we determined the BRAF mutation frequency in a panel of 13 mucosal melanomas and compared those data with data from all currently published series of cutaneous melanomas.

METHODS

BRAF exon 15 DNA from 13 archival primary mucosal melanomas (eight vulvar, four anorectal, and one laryngeal) was sequenced using intron-based primers. As archival DNA occasionally produces poor-quality template, results were confirmed with a TspRI restriction fragment length polymorphism (RFLP) that distinguishes wild-type BRAF from the common mutant form V599E. A binomial test was used to compare the mutation frequency in the mucosal melanomas with the published mutation frequency in cutaneous melanomas.

RESULTS

None of the 13 mucosal melanomas in this series had an exon 15 BRAF mutation, as compared to 54/165 (33%) primary cutaneous melanomas with BRAF mutations in a compilation of all current published studies (p = 0.006).

DISCUSSION

These data suggest that UV exposure, plays a role in the genesis of BRAF mutations in cutaneous melanoma, despite the absence of the characteristic C>T or CC>TT mutation signature associated with UV exposure, and suggests mechanisms other than pyrimidine dimer formation are important in UV-induced mutagenesis.

Model for the voltage steps in the breakdown of the integer quantum Hall effect

In samples used to maintain the U.S. resistance standard the breakdown of the dissipationless integer quantum Hall effect occurs as a series of dissipative voltage steps. A mechanism for this type of breakdown is proposed, based on the generation of magnetoexcitons when the quantum Hall fluid flows past an ionized impurity above a critical velocity. The calculated generation rate gives a voltage step height in good agreement with measurements on both electron and hole gases. We also compare this model to a hydrodynamic description of breakdown.

Creation of solitons and vortices by bragg reflection of Bose-Einstein condensates in an optical lattice

We study the dynamics of Bose-Einstein condensates in an optical lattice and harmonic trap. The condensates are set in motion by displacing the trap and initially follow simple semiclassical paths, shaped by the lowest energy band. Above a critical displacement, the condensate undergoes Bragg reflection. For high atom densities, the first Bragg reflection generates a train of solitons and vortices, which destabilize the condensate and trigger explosive expansion. At lower densities, soliton and vortex formation requires multiple Bragg reflections, and damps the center-of-mass motion.

The effect of ad libitum ingestion of a caffeinated carbohydrate-electrolyte solution on urinary caffeine concentration after 4 hours of endurance exercise

The purpose of the present study was to examine the effect of ad libitum ingestion of a carbohydrate-electrolyte solution (CES) with 150 mg x L (-1) caffeine (CAF) on urinary CAF concentration after 4 h of endurance exercise. Fifty-eight healthy and well-trained male subjects ingested ad libitum a 7 % CES with 150 mg x L (-1) CAF during 4 h cycling at 50 % of maximal work capacity. Total fluid consumption (mean +/- SE) was 2799 +/- 72 mL and CAF intake was 420 +/- 11 mg (5.7 +/- 0.2 mg x kg (-1) body weight). The post-exercise urinary CAF concentration (4.53 +/- 0.25 microg x mL (-1)) was below the doping level of the International Olympic Committee (12 microg x mL (-1)) in all subjects (range 1.20 - 10.84 microg x mL (-1)). A highly positive correlation was observed between CAF intake and post-exercise urinary CAF concentration (r = 0.68, p < 0.001). It is concluded that ad libitum ingestion of a CES with 150 mg x L (-1) CAF during 4 h cycling resulted in post-exercise urinary concentration below the doping level in all subjects.

Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir

BACKGROUND

The use of abacavir--a potent HIV-1 nucleoside-analogue reverse-transcriptase inhibitor--is complicated by a potentially life-threatening hypersensitivity syndrome in about 5% of cases. Genetic factors influencing the immune response to abacavir might confer susceptibility. We aimed to find associations between MHC alleles and abacavir hypersensitivity in HIV-1-positive individuals treated with abacavir.

METHODS

MHC region typing was done in the first 200 Western Australian HIV Cohort Study participants exposed to abacavir. Definite abacavir hypersensitivity was identified in 18 cases, and was excluded in 167 individuals with more than 6 weeks' exposure to the drug (abacavir tolerant). 15 individuals experienced some symptoms but did not meet criteria for abacavir hypersensitivity. p values were corrected for comparisons of multiple HLA alleles (p(c)) by multiplication of the raw p value by the estimated number of HLA alleles present within the loci examined.

FINDINGS

HLA-B*5701 was present in 14 (78%) of the 18 patients with abacavir hypersensitivity, and in four (2%) of the 167 abacavir tolerant patients (odds ratio 117 [95% CI 29-481], p(c)<0.0001), and the HLA-DR7 and HLA-DQ3 combination was found in 13 (72%) of hypersensitive and five (3%) of tolerant patients (73 [20-268], p(c)<0.0001 ). HLA-B*5701, HLA-DR7, and HLA-DQ3 were present in combination in 13 (72%) hypersensitive patients and none of the tolerant patients (822 [43-15 675], p(c)<0.0001). Other MHC markers also present on the 57.1 ancestral haplotype to which the three markers above belong confirmed the presence of haplotype-specific linkage disequilibrium, and mapped potential susceptibility loci to a region bounded by C4A6 and HLA-C. Within the entire abacavir-exposed cohort (n=200), presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 had a positive predictive value for hypersensitivity of 100%, and a negative predictive value of 97%.

INTERPRETATION

Genetic susceptibility to abacavir hypersensitivity is carried on the 57.1 ancestral haplotype. In our population, withholding abacavir in those with HLA-B*5701, HLA-DR7, and HLA-DQ3 should reduce the prevalence of hypersensitivity from 9% to 2.5% without inappropriately denying abacavir to any patient.

Screening for pre-eclampsia and fetal growth restriction by uterine artery Doppler at 11-14 weeks of gestation

OBJECTIVE

To examine the value of uterine artery Doppler at 11-14 weeks of gestation in the identification of women at risk of developing pre-eclampsia and fetal growth restriction.

METHODS

Uterine artery Doppler was carried out at 11-14 weeks in 3324 consecutive singleton pregnancies attending for routine care in three London hospitals. The right and left uterine arteries were identified using color flow mapping and velocity waveforms were obtained using pulsed Doppler. The mean pulsatility index of the two arteries was determined and the predictive value of a mean pulsatility index > the 95th centile in the prediction of pre-eclampsia and/or fetal growth restriction was calculated.

RESULTS

Satisfactory flow velocity waveforms were obtained from both uterine arteries in 3195 (96.1%) of the 3324 pregnancies examined and complete outcome information was obtained for 3045 (95.3%) of these women. The 95th centile of the uterine artery mean pulsatility index was 2.35 and did not change significantly with gestational age. The pregnancy was complicated by pre-eclampsia in 63 (2.1%) cases and by fetal growth restriction in 290 (9.5%) cases. The sensitivity of a mean pulsatility index > 2.35 for pre-eclampsia (with or without fetal growth restriction) was 27.0% but for fetal growth restriction alone it was 11.7%. The respective sensitivities for these complications requiring delivery before 32 weeks of gestation were 60.0% and 27.8%, respectively.

CONCLUSION

Uterine artery Doppler at 11-14 weeks of gestation identifies a high proportion of women who develop severe pre-eclampsia and/or fetal growth restriction.

Germline mutations in BRCA1 and BRCA2 in breast-ovarian families from a breast cancer risk evaluation clinic

PURPOSE

Data from the Breast Cancer Linkage Consortium suggest that the proportion of familial breast and ovarian cancers linked to BRCA1 or BRCA2 may be as high as 98% depending on the characteristics of the families, suggesting that mutations in BRCA1 or BRCA2 may entirely account for hereditary breast and ovarian cancer families. We sought to determine what proportion of families with both breast and ovarian cancers seen in a breast cancer risk evaluation clinic are accounted for by coding region germline mutations in BRCA1 and BRCA2 as compared to a linkage study group. We also evaluated what clinical parameters were predictive of mutation status.

PATIENTS AND METHODS

Affected women from 100 families with at least one case of breast cancer and at least one case of ovarian cancer in the same lineage were screened for germline mutations in the entire coding regions of BRCA1 and BRCA2 by conformation-sensitive gel electrophoresis, a polymerase chain reaction-based heteroduplex analysis, or direct sequencing.

RESULTS

Unequivocal deleterious mutations were found in 55% (55 of 100) of the families studied. Mutations in BRCA1 and BRCA2 accounted for 80% and 20% of the mutations overall, respectively. Using multivariate analysis, the strongest predictors of detecting a mutation in BRCA1 or BRCA2 in this study group were the presence of a single family member with both breast and ovarian cancer (P <.0009; odds ratio [OR], 5.68; 95% confidence interval [CI], 2.04 to 15.76) and a young average age at breast cancer diagnosis in the family (P <.0016; OR, 1.69; 95% CI, 1.23 to 2.38).

CONCLUSION

These results suggest that at least half of breast/ovarian families evaluated in a high-risk cancer evaluation clinic may have germline mutations in BRCA1 or BRCA2. Whether the remaining families have mutations in noncoding regions in BRCA1, mutations in other, as-yet-unidentified, low-penetrance susceptibility genes, or represent chance clustering remains to be determined.

Antibody recognition of melphalan adducts characterized using immobilized DNA: enhanced alkylation of G-Rich regions in cells compared to in vitro

The bifunctional alkylating agent, melphalan, forms adducts on DNA that are recognized by two previously described monoclonal antibodies, MP5/73 and Amp4/42. Immunoreactivity to MP5/73 was lost when alkylated DNA was exposed to alkaline pH, while Amp4/42 only recognized the structures formed after the alkali treatment. Competitive enzyme-linked immunoadsorbent assays (ELISAs) indicated that in 0.01 and 0.1 M NaOH, loss of immunoreactivity to MP5/73 occurred with half-lives that were at least 2-fold longer than half-lives for gain of immunoreactivity to Amp4/42. This supported previously published evidence that Amp4/42 did not simply recognize all the products formed by alkali treatment of adducts that were initially recognized by MP5/73. Adducts recognized by MP5/73 on RNA were considerably more stable at 100 degrees C and pH 7 than adducts on DNA. This was consistent with the hypothesis that immunorecognition involved N7 guanine adducts and ruled out the involvement of phosphotriesters in immunoreactivity. Synthetic oligodeoxyribonucleotides, covalently immobilized onto 96-well plates, were reacted with melphalan and incubated for various periods with alkali, and then the levels of adducts recognized by each antibody in replicate wells were assayed by a direct binding ELISA. Adducts formed on oligodeoxyguanylic acid were recognized very weakly by Amp4/42, unlike other DNA sequences that were tested. Retention of immobilized DNA during alkali treatment was confirmed by immunoassay of cisplatin adducts. Poor recognition by Amp4/42 of adducts in oligodeoxyguanylic acid was confirmed by a competitive ELISA. Amp4/42, unlike MP5/73, efficiently recognized adducts resulting from alkylation of DNA with chlorambucil. It is concluded that the two antibodies recognized melphalan adducts in different DNA sequence environments and that this explains (a) the different alkali stability of immunoreactive adducts and (b) previous results which showed that, in DNA from melphalan-treated cells, adducts recognized by Amp4/42 formed a smaller proportion of total adducts compared to DNA alkylated in vitro. The results presented here indicate that this was caused by a marked cellular influence on the overall sequence-dependent pattern of DNA alkylation or repair.

Screening for genomic rearrangements in families with breast and ovarian cancer identifies BRCA1 mutations previously missed by conformation-sensitive gel electrophoresis or sequencing

The frequency of genomic rearrangements in BRCA1 was assessed in 42 American families with breast and ovarian cancer who were seeking genetic testing and who were subsequently found to be negative for BRCA1 and BRCA2 coding-region mutations. An affected individual from each family was tested by PCR for the exon 13 duplication (Puget et al. 1999a) and by Southern blot analysis for novel genomic rearrangements. The exon 13 duplication was detected in one family, and four families had other genomic rearrangements. A total of 5 (11. 9%) of the 42 families with breast/ovarian cancer who did not have BRCA1 and BRCA2 coding-region mutations had mutations in BRCA1 that were missed by conformation-sensitive gel electrophoresis or sequencing. Four of five families with BRCA1 genomic rearrangements included at least one individual with both breast and ovarian cancer; therefore, 4 (30.8%) of 13 families with a case of multiple primary breast and ovarian cancer had a genomic rearrangement in BRCA1. Families with genomic rearrangements had prior probabilities of having a BRCA1 mutation, ranging from 33% to 97% (mean 70%) (Couch et al. 1997). In contrast, in families without rearrangements, prior probabilities of having a BRCA1 mutation ranged from 7% to 92% (mean 37%). Thus, the prior probability of detecting a BRCA1 mutation may be a useful predictor when considering the use of Southern blot analysis for families with breast/ovarian cancer who do not have detectable coding-region mutations.

Association of HPC2/ELAC2 genotypes and prostate cancer

HPC2/ELAC2 has been identified as a prostate cancer (CaP) susceptibility gene. Two common missense variants in HPC2/ELAC2 have been identified: a Ser-->Leu change at amino acid 217, and an Ala-->Thr change at amino acid 541. Tavtigian et al. reported that these variants were associated with CaP in a sample of men drawn from families with hereditary CaP. To confirm this report in a sample unselected for family history, we studied 359 incident CaP case subjects and 266 male control subjects that were frequency matched for age and race and were identified from a large health-system population. Among control subjects, the Thr541 frequency was 2.9%, and the Leu217 frequency was 31.6%, with no significant differences in frequency across racial groups. Thr541 was only observed in men who also carried Leu217. The probability of having CaP was increased in men who carried the Leu217/Thr541 variants (odds ratio = 2.37; 95% CI 1.06-5.29). This risk did not differ significantly by family history or race. Genotypes at HPC2/ELAC2 were estimated to cause 5% of CaP in the general population of inference. These results suggest that common variants at HPC2/ELAC2 are associated with CaP risk in a sample unselected for family history or other factors associated with CaP risk.

Genetic and hormonal risk factors in breast cancer

Breast cancer poses a serious public health problem, and it is hoped that identification of genetic and environmental factors that contribute to the development of breast cancer will enhance prevention efforts. Two breast cancer susceptibility genes (BRCA1 and BRCA2) have been identified, and germline mutations in these genes are thought to account for between 5% and 10% of all breast cancer cases. Current findings suggest that mutations in other highly penetrant genes may play an important role in breast cancer susceptibility, and studies aimed at the isolation of these genes are under way. In addition, common variants in a number of gene classes are thought to act as low-penetrance susceptibility alleles, and efforts to identify and characterize these variants are under way. This review discusses the genetic components of susceptibility to breast cancer from the standpoint of both human genetics and rat models.

The mouse as a model for the effects of MHC genes on human disease

As mice are often used to model human major histocompatibility complex (MHC)-associated diseases, it is important to understand how their MHC regions differ at the DNA level. The sequencing of the mouse MHC (H2 region) has enabled a detailed map of this region to be assembled for comparison with the human MHC. Here, Richard Allcock and colleagues outline the similarities between the human and mouse MHC regions and discuss notable differences that might affect disease models.

Coulomb-induced positive current-current correlations in normal conductors

In the white-noise limit current correlations measured at different contacts of a mesoscopic conductor are negative due to the antisymmetry of the wave function (Pauli principle). We show that current fluctuations at capacitive contacts induced via the long range Coulomb interaction due to charge fluctuations in the mesoscopic sample can be positively correlated. The positive correlations are a consequence of the extension of the wave functions into areas near both contacts. As an example we investigate in detail a quantum point contact in a high magnetic field under conditions in which transport is along an edge state.

The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster

Natural killer (NK) immunoglobulin-like receptors (KIRs) are a family of polymorphic receptors which interact with specific motifs on HLA class I molecules and modulate NK cytolytic activity. In this study, we analyzed a recently sequenced subgenomic region on chromosome 19q13.4 containing eight members of the KIR receptor repertoire. Six members are clustered within a 100-kb continuous sequence. These genes include a previously unpublished member of the KIR gene family 2DS6, as well as 2DL1, 2DL4, 3DL1, 2DS4, 3DL2, from centromere to telomere. Two additional KIR genes, KIRCI and 2DL3, which may be located centromeric of this cluster were also analyzed. We show that the KIR genes have undergone repeated gene duplications. Diversification between the genes has occurred postduplication primarily as a result of retroelement indels and gene truncation. Using pre- and postduplication Alu sequences identified within these genes as evolutionary molecular clocks, the evolution and duplication of this gene cluster is estimated to have occurred 30-45 million years ago, during primate evolution. A proposed model of the duplication history of the KIR gene family leading to their present organization is presented.

A comparison of some clinical features of visual reinforcement audiometry and the distraction test

The aim of this study was to compare aspects of visual reinforcement audiometry (VRA) and the distraction test (DT), the two most commonly used behavioural tests of hearing for young children. The number of assessments completed, time taken, parental opinion and levels of minimum responses were compared in a group of 20 infants (mean age 17.7 months; SD 4.7 months; range 12-25 months) who had been selected from those referred from a local second-tier community audiology service. Each infant was assessed with each test following set protocols and a balanced design on two occasions separated by one week. Parental opinion was determined by application of two questionnaires, one after each session. There was no difference in the number of minimum response levels (MRLs) measured by the two tests. However, if a VRA protocol using three MRLs was assumed then the assessment was completed successfully in a significantly greater number of subjects with VRA. VRA took, on average, two minutes less than the DT to measure six MRLs. Most of the subject sample had normal hearing as defined by both tests. However, where MRLs were >30 dB HL for at least one of the tests, the DT elicited responses at significantly higher levels than VRA, suggesting that in these subjects the DT under-estimated hearing sensitivity. Seventy per cent of parents selected VRA when asked to choose between the tests.

Diabetes-prone and diabetes-resistant BB rats share a common major diabetes susceptibility locus, iddm4: additional evidence for a "universal autoimmunity locus" on rat chromosome 4

Diabetes-prone (DP) BB rats develop autoimmune type 1 diabetes spontaneously. At least five loci are linked to disease expression: the major histocompatibility complex (iddm2), two susceptibility loci (iddm4, iddm5), and, possibly, a resistance locus (iddm3). Spontaneous disease also requires homozygosity for lyp/iddm1, which causes lymphopenia. It has not been determined whether lyp/iddm1 is required for predisposition to diabetes autoimmunity in addition to being required for its spontaneous expression. We analyzed backcross rats segregating for diabetes but not lymphopenia using Wistar-Furth (WF) and diabetes-resistant (DR) BB animals. The latter are nonlymphopenic (lyp+/+) and develop diabetes only in response to immunological perturbants. Treatment of (DR-BB x WF)F1 x WF animals (all lyp+/+) using a standard induction protocol caused type 1 diabetes in 58% of progeny. Expression of type 1 diabetes was strongly linked to iddm4. The results suggest that lyp/iddm1 does not determine the predisposition to autoimmunity in BB rats and that iddm4 is a major diabetogenic locus in both DP- and DR-BB animals. The iddm4 gene maps to a region containing several major autoimmunity loci, including aia2, aia3, and cia3. We propose that BB rat diabetes requires 1) class II RT1u (iddm2) for susceptibility, 2) additional loci for disease initiation and progression in response to perturbants, and 3) lyp for spontaneous disease.

Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease

Measurements of binding equilibria of EcoRV endonuclease to DNA, for a series of base-analogue substrates, demonstrate that expression of sequence selectivity is strongly enhanced by the presence of Ca2+ ions. Binding constants were determined for short duplex oligodeoxynucleotides containing the cognate DNA site, three cleavable noncognate sites, and a fully nonspecific site. At pH 7.5 and 100 mM NaCl, the full range of specificity from the specific (tightest binding) to nonspecific (weakest binding) sites is 0.9 kcal/mol in the absence of metal ions and 5.8 kcal/mol in the presence of Ca2+. Precise determination of binding affinities in the presence of the active Mg2+ cofactor was found to be possible for substrates retaining up to 1.6% of wild-type activity, as determined by the rate of phosphoryl transfer. These measurements show that Ca2+ is a near-perfect analogue for Mg2+ in binding reactions of the wild-type enzyme with DNA base-analogue substrates, as it provides identical DeltaDeltaG degrees bind values among the cleavable noncognate sites. Equilibrium dissociation constants of wild-type and base-analogue sites were also measured for the weakly active EcoRV mutant K38A, in the presence of either Mg2+ or Ca2+. In this case, Ca2+ allows expression of a greater degree of specificity than does Mg2+. DeltaDeltaG degrees bind values of K38A toward specific versus nonspecific sites are 6.1 kcal/mol with Ca2+ and 3.9 kcal/mol with Mg2+, perhaps reflecting metal-specific conformational changes in the ground-state ternary complexes. The enhancement of binding specificity provided by divalent metal ions is likely to be general to many restriction endonucleases and other metal-dependent nucleic acid-modifying enzymes. These results strongly suggest that measurements of DNA binding affinities for EcoRV, and likely for many other restriction endonucleases, should be performed in the presence of divalent metal ions.

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.

Non-major histocompatibility complex-linked diabetes susceptibility loci on chromosomes 4 and 13 in a backcross of the DP-BB/Wor rat to the WF rat

BB rats are used as models of autoimmune human IDDM. Genetic control of IDDM in both species is complex, including both major histocompatibility complex (MHC)-linked and non-MHC-linked genes. DP-BB rats develop IDDM spontaneously. Expression of disease in these animals requires homozygosity at the lyp locus, which causes lymphopenia. All genetic analyses of BB rat diabetes to date have backcrossed to the DP-BB strain or used (DP-BB x non-BB)F2 animals to ensure that a fraction of progeny are homozygous for lyp. Here we report the analysis of a backcross of the DP-BB rat to the histocompatible WF rat. Neither WF nor (WF x DP-BB)F1 animals develop spontaneous IDDM. However, 95% of (WF x DP-BB)F1 rats and a fraction of (WF x DP-BB) x WF backcross animals readily develop IDDM after treatment with polyinosinic:polycytidylic acid and a cytotoxic anti-RT6.1 monoclonal antibody. Using simple sequence length polymorphism analysis, we have mapped loci on chromosomes 4 and 13 that show significant linkage to IDDM expression and insulitis. The susceptibility locus on chromosome 4 is linked to, but not identical to, lyp. We propose a disease model for the BB rat that requires 1) the RT1u MHC haplotype for disease susceptibility, 2) a new locus on chromosome 4 for disease initiation (as measured by insulitis), 3) a new locus on chromosome 13 for disease progression in response to environmental perturbation, and 4) lyp for spontaneous expression of disease.

Classifying a protein in the CATH database of domain structures

The CATH database of protein domain structures classifies structures according to their (C)lass, (A)rchitecture, (T)opology or fold and (H)omologous family (http://www.biochem.ucl.ac.uk/bsm/cath). Although the protocol used is mostly automatic, manual inspection is used to check assignments at some critical stages, such as the detection of very distantly related homologues and anologues and the assignment of novel architectures. Described in this article is a recently established facility to search the database with the coordinates of a newly determined structure. The CATH server first locates domain boundaries and then uses automatic sequence and structure comparison methods to assign this new structure to one or more of the domain families within CATH. Diagnostic reports are generated, together with multiple structural alignments for close relatives. The Server can be accessed over the World Wide Web (WWW) and mirror sites are planned to improve access.

Monocyte chemoattractant protein-1-induced CCR2B receptor desensitization mediated by the G protein-coupled receptor kinase 2

Monocyte chemoattractant protein 1 (MCP-1) is a member of the chemokine cytokine family, whose physiological function is mediated by binding to the CCR2 and CCR4 receptors, which are members of the G protein-coupled receptor family. MCP-1 plays a critical role in both activation and migration of leukocytes. Rapid chemokine receptor desensitization is very likely essential for accurate chemotaxis. In this report, we show that MCP-1 binding to the CCR2 receptor in Mono Mac 1 cells promotes the rapid desensitization of MCP-1-induced calcium flux responses. This desensitization correlates with the Ser/Thr phosphorylation of the receptor and with the transient translocation of the G protein-coupled receptor kinase 2 (GRK2, also called beta-adrenergic kinase 1 or betaARK1) to the membrane. We also demonstrate that GRK2 and the uncoupling protein beta-arrestin associate with the receptor, forming a macromolecular complex shortly after MCP-1 binding. Calcium flux responses to MCP-1 in HEK293 cells expressing the CCR2B receptor were also markedly reduced upon cotransfection with GRK2 or the homologous kinase GRK3. Nevertheless, expression of the GRK2 dominant-negative mutant betaARK-K220R did not affect the initial calcium response, but favored receptor response to a subsequent challenge by agonists. The modulation of the CCR2B receptor by GRK2 suggests an important role for this kinase in the regulation of monocyte and lymphocyte response to chemokines.

Optimization of Phaffia rhodozyma continuous culture through response surface methodology

Response surface methodology was applied to optimize the growth of the yeast Phaffia rhodozyma in continuous fermentation using peat hydrolysates as substrate. A second-order, complete, factorial design of the experiments was used to develop empirical models providing a quantitative interpretation of the relationships between the two variables studied, dilution rate and pH. Maximum biomass concentration in the fermentor was obtained by employing the following predicted optimum fermentation conditions: a dilution rate of 0.017/h and a pH level of 7.19. A verification experiment, conducted at previously optimized conditions for maximum biomass volumetric productivity (a dilution rate of 0.022/h, and a pH level of 6.90), produced values for biomass concentration, residual substrate concentration, biomass yield, and biomass volumetric productivity that were very close to the predicted values, indicating the reliability of the empirical model. The concentration of the pigment astaxanthin produced by the yeast under the optimized growth conditions was found to be 544 mg astaxanthin/kg dry cell biomass.

Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis

The structures of wild-type and mutant forms of the unliganded EcoRV endonuclease dimer have been determined at 2.4 A resolution in a new crystal lattice. Comparison of these structures with that of the free enzyme determined with different packing constraints shows that the conformations of the domain interfaces are not conserved between crystal forms. The unliganded enzyme and the enzyme-DNA complex delineate two distinct quaternary states separated by a 25 degrees intersubunit rotation, but considerable conformational heterogeneity, of the order of 10 degrees domain rotations, exists within each of these states. Comparison of the free enzyme structure between the two crystal forms further reveals that the C-terminal 28 amino acid residues are disordered and undergo an extensive local folding transition upon DNA binding. Introduction of the mutation T93A at the DNA-binding cleft causes large-scale effects on the protein conformation. Structural changes in the mutated unliganded enzyme propagate some 20 to 25 A to the dimerization interface and lead to a rearrangement of monomer subunits. Comparative analysis of these structures, a new structure of the enzyme cocrystallized with DNA and calcium ions, and previously determined cocrystal structures suggests important roles for a number of amino acid residues in facilitating the intersubunit motions and local folding transitions. In particular, the T93A structure reveals a pathway through the protein, by which DNA-binding may cause the domain movements required for proper alignment of catalytic groups. The key active-site residue Glu45 is located on a flexible helix inside this pathway, and this provides a direct means by which essential catalytic functions are coupled to the protein conformational change. It appears that indirect perturbation of the Glu45 conformation via an altered quaternary structure may be a contributing factor to the decreased catalytic efficiency of T93A, and this mechanism may also explain the diminished activities of other active site variants of EcoRV.