Population consequences of a predator-induced habitat shift by trout in whole-lake experiments

In a replicated whole-lake experiment, we (a) tested for the existence of a flexible habitat shift in response to predator presence in age-0 rainbow trout (Oncorhynchus mykiss) at risk of cannibalism and (b) evaluated the population-level consequences of habitat shifts in terms of growth and survival over their first growing season. Daphnid food and adult trout predators were substantially more abundant in pelagic than in littoral habitats. Age-0 trout used all habitats in populations without adult trout predators, whereas age-0 trout were observed only in the less profitable littoral habitat in populations with adult trout. Consequently, mean fall mass of age-0 trout in the presence of predators was almost half that observed in populations without adult trout. Despite the shift in habitat use, age-0 trout experienced 90% mortality when adult trout predators were present, in comparison to only 36% mortality when absent. We conclude that the commonly observed habitat shifts by fish at risk of predation, observed at smaller scales, do in fact occur at the whole-system scale over long time intervals. These results suggest that fish are able to perceive risk at large spatial scales and thus take advantage of profitable (but normally risky) habitats when predators are absent, or move to less profitable refuge habitats when predators are present.

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

Rapid detection of SMARCB1 sequence variation using high resolution melting

Background : Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Methods : Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results : The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions : This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening.

The effects of whole-body vibration on the cross-transfer of strength

This study investigated whether the use of superimposed whole-body vibration (WBV) during cross-education strength training would optimise strength transfer compared to conventional cross-education strength training. Twenty-one healthy, dominant right leg volunteers (21±3 years) were allocated to a strength training (ST, m = 3, f = 4), a strength training with WBV (ST + V, m = 3, f = 4), or a control group (no training, m = 3, f = 4). Training groups performed 9 sessions over 3 weeks, involving unilateral squats for the right leg, with or without WBV (35 Hz; 2.5mm amplitude). All groups underwent dynamic single leg maximum strength testing (1RM) and single and paired pulse transcranial magnetic stimulation (TMS) prior to and following training. Strength increased in the trained limb for the ST (41%; ES = 1.14) and ST + V (55%; ES = 1.03) groups, which resulted in a 35% (ES = 0.99) strength transfer to the untrained left leg for the ST group and a 52% (ES = 0.97) strength transfer to the untrained leg for the ST + V group, when compared to the control group. No differences in strength transfer between training groups were observed (P = 0.15). For the untrained leg, no differences in the peak height of recruitment curves or SICI were observed between ST and ST + V groups (P = 1.00). Strength training with WBV does not appear to modulate the cross-transfer of strength to a greater magnitude when compared to conventional cross-education strength training.

Frequency of excisions and yields of malignant skin tumors in a population-based screening intervention of 360 288 whole-body examinations

Objective To explore the frequency of excisions and yields of histopathologically confirmed skin cancer.

Design A population-based skin cancer screening intervention (the SCREEN project) in the German state of Schleswig-Holstein (July 1, 2003, to June 30, 2004).

Setting Physician offices. Participants could choose between nondermatologist physicians and dermatologists for their initial whole-body skin examination. All screening physicians received a mandatory 8-hour training course.

Participants Inhabitants of Schleswig-Holstein 20 years or older with statutory health insurance (N = 360 288).

Main Outcome Measures Frequency of excisions and yields of malignant skin tumors (malignant melanomas [MMs], basal cell carcinomas [BCCs], and squamous cell carcinomas [SCCs]), stratified by sex and age.

Results Overall, 15 983 excisions were performed (1 of 23 screenees). A total of 3103 malignant skin tumors were diagnosed in 2911 persons: 585 MMs, 1961 BCCs, 392 SCCs, and 165 other malignant skin tumors. Overall, 116 persons (3103 of 360 288) had to be screened to find 1 malignant tumor, with 1 of 620 for MM, 1 of 184 for BCC, and 1 of 920 for SCC. Twenty excisions were performed to find 1 melanoma in men 65 years and older, but more than 50 excisions were required to find 1 melanoma in men aged between 20 and 49 years.

Conclusions The results of SCREEN suggest a high yield of malignant skin tumors in a large-scale population-based screening project. We found that a high number of excisions was performed in the youngest screenees with an associated low yield, suggesting a need in screener training to emphasize a more conservative attitude toward excisions in young screenees.

Coupled RNA polymerase II transcription and 3′ end formation with yeast whole-cell extracts

 RNA polymerase II (RNAP II) transcription and pre-mRNA 3' end formation are linked through physical and functional interactions. We describe here a highly efficient yeast in vitro system that reproduces both transcription and 3' end formation in a single reaction. The system is based on simple whole-cell extracts that were supplemented with a hybrid Gal4-VP16 transcriptional activator and supercoiled plasmid DNA templates encoding G-less cassette reporters. We found that the coupling of transcription and processing in vitro enhanced pre-mRNA 3' end formation and reproduced requirements for poly(A) signals and polyadenylation factors. Unexpectedly, however, we show that in vitro transcripts lacked m⁷G-caps. Reconstitution experiments with CF IA factor assembled entirely from heterologous components suggested that the CTD interaction domain of the Pcf11 subunit was required for proper RNAP II termination but not 3' end formation. Moreover, we observed reduced termination activity associated with extracts prepared from cells carrying a mutation in the 5'-3' exonuclease Rat1 or following chemical inhibition of exonuclease activity. Thus, in vitro transcription coupled to pre-mRNA processing recapitulates hallmarks of poly(A)-dependent RNAP II termination. The in vitro transcription/processing system presented here should provide a useful tool to further define the role of factors involved in coupling.

Effectiveness of alternative organic solvents in field preservation of whole barnacles for PCR analyses

There are few reports of non-cryogenic preservation methods for marine invertebrates, so potable alcohol and acetone-based nail varnish remover (NVR) are for the first time evaluated against absolute ethanol as short-term preservatives of whole barnacles. Performance of ethanol and NVR-preserved material was comparable, but potable alcohol was significantly worse. These results are of practical importance for fieldwork in remote areas where laboratory chemicals are unattainable but potable alcohol or NVR are locally available. Of these, acetone-based NVR would be the solvent of preference.

The small molecule, genistein, increases hepcidin expression in human hepatocytes

Hepcidin, a peptide hormone that decreases intestinal iron absorption and macrophage iron release, is a potential drug target for patients with iron overload syndromes because its levels are inappropriately low in these individuals. Endogenous stimulants of Hepcidin transcription include bone morphogenic protein 6 (BMP6) and interleukin-6 (IL-6) by effects on mothers against decapentaplegic homolog (Smad)4 or signal transducer and activator of transcription (Stat)3, respectively. We conducted a small-scale chemical screen in zebrafish embryos to identify small molecules that modulate hepcidin expression. We found that treatment with the isoflavone, genistein, from 28-52 hours postfertilization in zebrafish embryos enhanced Hepcidin transcript levels, as assessed by whole-mount in situ hybridization and quantitative real-time reverse-transcriptase polymerase chain reaction. Genistein's stimulatory effect was conserved in human hepatocytes: Genistein treatment of HepG2 cells increased both Hepcidin transcript levels and promoter activity. We found that genistein's effect on Hepcidin expression did not depend on estrogen receptor signaling or increased cellular iron uptake, but was impaired by mutation of either BMP response elements or the Stat3-binding site in the Hepcidin promoter. RNA sequencing of transcripts from genistein-treated hepatocytes indicated that genistein up-regulated 68% of the transcripts that were up-regulated by BMP6; however, genistein raised levels of several transcripts involved in Stat3 signaling that were not up-regulated by BMP6. Chromatin immunoprecipitation and ELISA experiments revealed that genistein enhanced Stat3 binding to the Hepcidin promoter and increased phosphorylation of Stat3 in HepG2 cells. Conclusion: Genistein is the first small-molecule experimental drug that stimulates Hepcidin expression in vivo and in vitro. These experiments demonstrate the feasibility of identifying and characterizing small molecules that increase Hepcidin expression. Genistein and other candidate molecules may subsequently be developed into new therapies for iron overload syndromes.

The whole truth is both too much and not sufficient

Lawyers and fans of legal drama will recognise the phrase “the truth, the whole truth and nothing but the truth”. But relevance is also required. In a different context, students often mistakenly believe that quantity of truth will compensate for any deficiencies in quality and relevance.

The curricula of the various Australian jurisdictions, and the National Curriculum, encourage students to conduct research on the Internet. There is a wealth of good information on the Internet; there is also a lot of poor information. Students should learn to interrogate sources to discover if the author has expert knowledge in that area, and if the publisher or website has any quality assurance protocols.

Correctness and quantity of information does not compensate for deficiencies in quality and relevance. Useful scientific information has appropriate precision, accuracy and conciseness.

The Internet gives access to databases, to vast amounts of information, to primary and second-hand data, and to summaries and analyses of information. Nobel Laureate Linus Pauling often said that the use of computers is not a substitute for thinking, and the same is true of the Internet. Teachers will always be needed to guide students on the appropriate use of learning tools on the journey of discovery that we call education.