The influence of riparian woodland on the spatial and temporal variability of stream water temperatures in an upland salmon stream

International audienceThe spatio-temporal variability of stream water temperatures was investigated at six locations on the Girnock Burn (30km2 catchment), Cairngorms, Scotland over three hydrological years between 1998 and 2002. The key site-specific factors affecting the hydrology and climatology of the sampling points were investigated as a basis for physical process inference. Particular emphasis was placed on assessing the effects of riparian forest in the lower catchment versus the heather moorland riparian zones that are spatially dominant in the upper catchment. The findings were related to river heat budget studies that provided process detail. Gross changes in stream temperature were affected by the annual cycle of incoming solar radiation and seasonal changes in hydrological and climatological conditions. Inter-annual variation in these controlling variables resulted in inter-annual variability in thermal regime. However, more subtle inter-site differences reflected the impact of site-specific characteristics on various components of the river energy budget. Inter-site variability was most apparent at shorter time scales, during the summer months and for higher stream temperatures. Riparian woodland in the lower catchment had a substantial impact on thermal regime, reducing diel variability (over a period of 24 hours) and temperature extremes. Observed inter-site differences are likely to have a substantial effect on freshwater ecology in general and salmonid fish in particular. Keywords: temperature, thermal regime, forest, salmon, hydrology, Girnock Burn, Cairngor

Variability in stream discharge and temperature: a preliminary assessment of the implications for juvenile and spawning Atlantic salmon

This study focuses on understanding the temporal variability in hydrological and thermal conditions in a small mountain stream and its potential implication for two life stages of Atlantic salmon (<I>Salmo salar</I>) &ndash; stream resident juveniles and returning adult spawners. Stream discharge and temperature in the Girnock Burn, NE Scotland, were characterised over ten hydrological years (1994/1995&ndash;2003/2004). Attention was focussed on assessing variations during particular ecologically 'sensitive' time periods when selected life-stages of salmon behaviour may be especially influenced by hydrological and thermal conditions. <P style='line-height: 20px;'> Empirical discharge data were used to derive hydraulic parameters to predict the Critical Displacement Velocity (CDV) of juvenile salmon. This is the velocity above which fish may no longer be able to hold station in the water column and thus can be used as an index of time periods where feeding behaviour might be constrained. In the Girnock Burn, strong inter- and intra-annual variability in hydrological and thermal conditions may have important implications for feeding opportunities for juvenile fish; both during important growth periods in late winter and early spring, and the emergence of fry in the late spring. Time periods when foraging behaviour of juvenile salmon may be constrained by hydraulic conditions were assessed as the percentage time when CDV for 0+ and 1+ fish were exceeded by mean daily stream velocities. Clear seasonal patterns of CDV were apparent, with higher summer values driven by higher stream temperatures and fish length. Inter-annual variability in the time when mean stream velocity exceeded CDV for 0+ fish ranged between 29.3% (1997/1998) and 44.7% (2000/2001). For 1+ fish mean stream velocity exceeded CDV between 14.5% (1997/1998) and 30.7% (2000/2001) of the time. <P style='line-height: 20px;'> The movement of adult spawners into the Girnock Burn in preparation for autumn spawning (late October to mid-November) exhibited a complex relationship with hydrological variability with marked inter-annual contrasts. In years when discharge in the period prior to spawning was low, fish movement was increasingly triggered by suboptimal flow increases as spawning time approached. In contrast, wet years with numerous events allowed a much more even distribution of fish entry. Elucidating links between discharge/temperature variability and foraging opportunities and upriver migration of adult Atlantic salmon have the potential to contribute to the improvement of conservation strategies in both regulated and unregulated rivers

Factors influencing the opinion of individuals in determining tumour spread after biopsy

<p>Abstract</p> <p>Background</p> <p>People often have concerns regarding tumour spread after biopsy which leads to a delay in seeking expert medical advice. The data regarding this perception is scanty. Therefore, we conducted this cross sectional study to explore the beliefs and perceptions of individuals regarding tumour spread after biopsy and the basis of those beliefs.</p> <p>Methods</p> <p>The survey was conducted in outpatient areas of two different tertiary care hospitals of Karachi namely Aga Khan University Hospital Karachi (AKUH) and Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN). We interviewed 600 individuals and documented their responses on a questionnaire. There were 400 responders from Aga Khan's Consulting Clinic and 100 each from Aga Khan's Oncology Clinic and KIRAN.</p> <p>Results</p> <p>Only 50% of the respondents chose biopsy as the best test for diagnosis of cancer. The level of education was statistically significant in making this choice of answer (<it>p </it>= 0.02) only in univariate analysis. Those individuals who were involved in the work up of cancer patients irrespective of their educational status gave more intelligent answers (<it>p </it>= 0.003). The tumour disturbance after biopsy was regarded as a major factor among 127 respondents (53%) who believed that biopsy could lead to spread of tumour.</p> <p>Conclusions</p> <p>Our study revealed that awareness regarding cancer diagnosis and biopsy is lacking among general public and it does not co-relate well with the level of formal education. These misconception and taboos need to be addressed in public seminars and in the media in order to increase the awareness which could facilitate prompt diagnosis.</p

Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event

In humans and mice, there are 11 genes derived from sushi-ichi related retrotransposons, some of which are known to play essential roles in placental development. Interestingly, this family of retrotransposons was thought to exist only in eutherian mammals, indicating their significant contributions to the eutherian evolution, but at least one, PEG10, is conserved between marsupials and eutherians. Here we report a novel sushi-ichi retrotransposon-derived gene, SIRH12, in the tammar wallaby, an Australian marsupial species of the kangaroo family. SIRH12 encodes a protein highly homologous to the sushi-ichi retrotransposon Gag protein in the tammar wallaby, while SIRH12 in the South American short-tailed grey opossum is a pseudogene degenerated by accumulation of multiple nonsense mutations. This suggests that SIRH12 retrotransposition occurred only in the marsupial lineage but acquired and retained some as yet unidentified novel function, at least in the lineage of the tammar wallaby

Cost of Mating and Insemination Capacity of a Genetically Modified Mosquito Aedes aegypti OX513A Compared to Its Wild Type Counterpart

The idea of implementing genetics-based insect control strategies modelled on the traditional SIT is becoming increasingly popular. In this paper we compare a genetically modified line of Aedes aegypti carrying a tetracycline repressible, lethal positive feedback system (OX513A) with its wild type counterpart with respect to their insemination capacities and the cost of courtship and mating. Genetically modified males inseminated just over half as many females as the wild type males during their lifetime. Providing days of rest from mating had no significant effect on the total number of females inseminated by males of either line, but it did increase their longevity. Producing sperm had a low cost in terms of energy investment; the cost of transferring this sperm to a receptive female was much higher. Continued mating attempts with refractory females suggest that males could not identify refractory females before investing substantial energy in courtship. Although over a lifetime OX513A males inseminated fewer females, the number of females inseminated over the first three days, was similar between males of the two lines, suggesting that the identified cost of RIDL may have little impact on the outcome of SIT-based control programmes with frequent releases of the genetically modified males

Ductal carcinoma in situ and sentinel lymph node metastasis in breast cancer

<p>Abstract</p> <p>Background</p> <p>The impact of sentinel lymph node biopsy on breast cancer mimicking ductal carcinoma in situ (DCIS) is a matter of debate.</p> <p>Methods</p> <p>We studied the rate of occurrence of sentinel lymph node metastasis in 255 breast cancer patients with pure DCIS showing no invasive components on routine pathological examination. We compared this to the rate of occurrence in 177 patients with predominant intraductal-component (IDC) breast cancers containing invasive foci equal to or less than 0.5 cm in size.</p> <p>Results</p> <p>Most of the clinical and pathological baseline characteristics were the same between the two groups. However, peritumoral lymphatic permeation occurred less often in the pure DCIS group than in the IDC-predominant invasive-lesion group (1.2% vs. 6.8%, p = 0.002). One patient (0.39%) with pure DCIS had two sentinel lymph nodes positive for metastasis. This rate was significantly lower than that in patients with IDC-predominant invasive lesions (6.2%; p < 0.001).</p> <p>Conclusions</p> <p>Because the rate of sentinel lymph node metastasis in pure DCIS is very low, sentinel lymph node biopsy can safely be omitted.</p

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

Abstract Background The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. Methods A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Results Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. Conclusion We demonstrated that FFPE specimens retained important prognostic information that could be identified using a recent gene profiling technology. Our study supports the use of FFPE specimens for the development and refinement of prognostic gene signatures for breast cancer. Clinical applications of such prognostic gene profiles await future large-scale validation studies

Proteomic Analyses Reveal High Expression of Decorin and Endoplasmin (HSP90B1) Are Associated with Breast Cancer Metastasis and Decreased Survival

BACKGROUND: Breast cancer is the most common malignancy among women worldwide in terms of incidence and mortality. About 10% of North American women will be diagnosed with breast cancer during their lifetime and 20% of those will die of the disease. Breast cancer is a heterogeneous disease and biomarkers able to correctly classify patients into prognostic groups are needed to better tailor treatment options and improve outcomes. One powerful method used for biomarker discovery is sample screening with mass spectrometry, as it allows direct comparison of protein expression between normal and pathological states. The purpose of this study was to use a systematic and objective method to identify biomarkers with possible prognostic value in breast cancer patients, particularly in identifying cases most likely to have lymph node metastasis and to validate their prognostic ability using breast cancer tissue microarrays. METHODS AND FINDINGS: Differential proteomic analyses were employed to identify candidate biomarkers in primary breast cancer patients. These analyses identified decorin (DCN) and endoplasmin (HSP90B1) which play important roles regulating the tumour microenvironment and in pathways related to tumorigenesis. This study indicates that high expression of Decorin is associated with lymph node metastasis (p&lt;0.001), higher number of positive lymph nodes (p&lt;0.0001) and worse overall survival (p = 0.01). High expression of HSP90B1 is associated with distant metastasis (p&lt;0.0001) and decreased overall survival (p&lt;0.0001) these patients also appear to benefit significantly from hormonal treatment. CONCLUSIONS: Using quantitative proteomic profiling of primary breast cancers, two new promising prognostic and predictive markers were found to identify patients with worse survival. In addition HSP90B1 appears to identify a group of patients with distant metastasis with otherwise good prognostic features