Towards best practices in research: Role of academic core facilities

Academic Core Facilities are optimally situated to improve the quality of preclinical research by implementing quality control measures and offering these to their users. Subject Categories: Methods & Resources, Science Policy & Publishing

During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, ²⁰¹⁶; Bespalov & Steckler, ²⁰¹⁸; Heddleston et al, ²⁰²¹). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, ²⁰²¹). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference.It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting‐edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, ²⁰²⁰). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.     

Physiological tonicity improves human chondrogenic marker expression through nuclear factor of activated T-cells 5 <Emphasis Type="Italic">in vitro</Emphasis>

Introduction  

Chondrocytes experience a hypertonic environment compared with plasma (280 mOsm) due to the high fixed negative charge density of cartilage. Standard isolation of chondrocytes removes their hypertonic matrix, exposing them to nonphysiological conditions. During in vitro expansion, chondrocytes quickly lose their specialized phenotype, making them inappropriate for cell-based regenerative strategies. We aimed to elucidate the effects of tonicity during isolation and in vitro expansion on chondrocyte phenotype.     

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.     

A genetic assessment of seed production areas (SPAs) for restoration

The conservation and restoration of degraded landscapes continues to be a major activity with the demand for seed increasing to meet growing global targets. Seed collected from natural plant populations is often irregular and unpredictable, limiting the diversity of species that can be conserved through restoration programs and the area that can be restored. Seed production areas (SPAs; seed orchards, seed increase) are one option for improving seed supply and quality to meet the demand from conservation and restoration programs. We evaluated genetic diversity, inbreeding and mating system parameters in adults and seed from remnants and SPAs of Acacia montana and Dodonaea viscosa subsp. cuneata, two key restoration species in south-eastern Australia. Overall, we found no significant differences in genetic diversity between remnants and SPAs of both species or between adult and seed cohorts. In contrast, we found significant inbreeding in many remnants and their seed crops suggesting that some inbred seed were used to establish these SPAs. We also found significant inbreeding in some SPAs and their seed crops and that SPAs were often biased towards one to two source remnants. Additional germplasm is now required to broaden the representativeness of remnants in the SPAs and the genetic base of seed being produced for restoration programs.     

Pollen Dispersal in Fragmented Populations of the Dioecious Wind-Pollinated Tree,Allocasuarina verticillata (Drooping Sheoak,Drooping She-Oak; Allocasuarinaceae)

Vegetation clearing, land modification and agricultural intensification have impacted on many ecological communities around the world. Understanding how species respond to fragmentation and the scales over which functionality is retained, can be critical for managing biodiversity in agricultural landscapes. Allocasuarina verticillata (drooping sheoak, drooping she-oak) is a dioecious, wind-pollinated and -dispersed species with key conservation values across southeastern Australia. But vegetation clearing associated with agricultural expansion has reduced the abundance and spatial distribution of this species in many regions. Spatial genetic structure, relatedness among trees, pollen dispersal and mating patterns were examined in fragmented A. verticillata populations selected to represent the types of remnants that now characterise this species. Short scale spatial genetic structure (5–25 m) and relatedness among trees were observed in most populations. Unexpectedly, the two male trees closest to each female did not have a reproductive advantage accounting for only 4–15% of the seed produced in larger populations. Biparental inbreeding was also generally low (<4%) with limited evidence of seed crop domination by some male trees. More male trees contributed to seed crops in linear remnants (mean 17) compared to those from patch remnants (mean 11.3) which may reflect differences in pollen dispersal within the two remnant types. On average, pollen travels ~100 m irrespective of remnant type but was also detected to have dispersed as far as 1 km in open landscapes. Low biparental inbreeding, limited reproductive assurance for near-neighbour and probably related males and variability in the distances over which females sample pollen pools suggest that some mechanism to prevent matings between relatives exists in this species.     

Effects of Mesh Size and Escape Gaps on Discarding in an Australian Giant Mud Crab (Scylla serrata) Trap Fishery

In response to concerns over excessive discarding from Australian recreational round traps (with four funnel entrances) used to target giant mud crabs, Scylla serrata, an experiment was done to assess the independent and cumulative utility of paired, bottom-located horizontal escape gaps (46×120 mm) and increasing mesh size (from 51 to 101 mm). Compared to conventional traps comprising 51-mm mesh throughout, those with the same mesh size and escape gaps caught significantly fewer (by 95%) undersize (<85 mm carapace length – CL) crabs while maintaining legal catches. Traps made from 101-mm mesh (but with the same funnel entrances as conventional designs) and with and without escape gaps similarly retained fewer undersize crabs and also yellowfin bream Acanthopagrus australis (the key bycatch species) by up to 94%, but there were concomitant reductions in fishing power for legal sizes of S. serrata. Although there were no immediate mortalities among any discarded crabs, there was a greater bias towards wounding among post molts than late inter-molts and less damage to individuals in the 101-mm conventional than 51-mm conventional traps (without escape gaps). The results support retrospectively fitting escape gaps in conventional S. serrata traps as a means for reducing discarding, but additional work is required to determine appropriate mesh sizes/configurations that maximize species and size selectivity.     

Elf5 regulation in the trophectoderm

Mouse Elf5 is expressed exclusively in the trophectoderm from the late blastocyst stage to postgastrulation. We demonstrate here that the proximal promoter is used for trophectoderm expression but is not sufficient on its own. In transgenic assays, deletion of a differentially methylated region (DMR) within the promoter has no effect on the activation and maintenance of trophectoderm expression and does not result in ectopic activity. Two redundant enhancers drive Elf5 expression to the extraembryonic ectoderm and ectoplacental cone. The enhancers, located in the 5′ half of intron 1 and 3′ half of intron 2, require the presence of 1.8 kbp, although not the DMR, of the endogenous proximal promoter for optimal activity. These trophectoderm enhancers are mouse specific. A cattle Elf5 BAC reporter transgene is not expressed in mouse trophectoderm although it is expressed in skin, a known foetal domain of mouse Elf5 expression. The established importance of Elf5 for mouse trophectoderm at pre- and perigastrulation stages is not a conserved mammalian feature as Elf5 expression localises to embryonic as opposed to trophectodermal ectoderm in cattle.