Expectations for all: Universities and supervisors have a responsibility to manage PhD career prospects.

Athene Donald highlights an important document published by the Royal Society which addresses the plight of PhD students and their job prospects. The overall shape of the pipeline feeding through from research student to professor is not in doubt. Few make it. Supervisors and institutions can do more to manage expectations and improve job prospects. It is vital that students pick up other skills, look to broaden their CVs and gain a breadth of experience during their PhDs for the situation to improve

Foreword

If ever there was a time when scientists and policy-makers needed to work together, it is now during the COVID-19 pandemic. Scientific evidence can be hard to interpret; the balancing act that politicians spend their lives performing depends on more than this evidence because they care (possibly too much) about voters’ wishes. Appreciating the way these two, sometimes conflicting, trajectories interweave is crucial if a scientist is to be effective in the policy space. CUSPE and its work provide a wonderful way for students to examine these interactions first-hand and experience some of the challenges that they provide

The impact of environmental changes upon the microrheological response of adherent cells

International audienceThe mechanical behaviour of adherent cells cultured in vitro is known to be dependent on the mechanical properties of the substrate. We show that this mechanical behaviour is also strongly affected by the cells' environment. We focus here on the impact of temperature and pH. Experiments carried out on individual cells in a tuneable environment reveal that the intra-cellular mechanical behaviour exhibits large and fast changes when the external cell environment is changed. Fast passive microrheometry measurements allow for the precise characterisation of the transient regime observed during a temperature drop. When maintained at a non physiological temperature, the cells reach a stabilised state distinct from the state observed in physiological conditions. The perturbation can be reversed but exhibits hysteretic behaviour when physiological conditions are restored. The transient regime observed during the recovery process is found to be different from the transient regime observed when leaving physiological conditions. A modified generalized Stokes-Einstein equation taking into account the cell activity through an effective temperature is proposed here to fit the experimental results. Excellent agreement between the model and the measurements is obtained for time lags from 10 −3 to 1 s considered in this study. PACS. 87.17.Rt Cell adhesion and cell mechanics – 87.16.dm Mechanical properties and rheology – 87.16.Ln Cytoskeleto

Revealing the dependence of cell spreading kinetics on its spreading morphology using microcontact printed fibronectin patterns.

Since the dawn of in vitro cell cultures, how cells interact and proliferate within a given external environment has always been an important issue in the study of cell biology. It is now well known that mammalian cells typically exhibit a three-phase sigmoid spreading on encountering a substrate. To further this understanding, we examined the influence of cell shape towards the second rapid expansion phase of spreading. Specifically, 3T3 fibroblasts were seeded onto silicon elastomer films made from polydimethylsiloxane (PDMS), and micro-contact printed with fibronectin stripes of various dimensions. PDMS is adopted in our study for its biocompatibility, its ease in producing very smooth surfaces, and in the fabrication of micro-contact printing stamps. The substrate patterns are compared with respect to their influence on cell spreading over time. Our studies reveal, during the early rapid expansion phase, 3T3 fibroblasts are found to spread radially following a t≃¹·⁸ law; meanwhile, they proliferated in a lengthwise fashion on the striped patterns, following a t≃¹ law. We account for the observed differences in kinetics through a simple geometric analysis which predicted similar trends. In particular, a t² law for radial spreading cells, and a t¹ law for lengthwise spreading cells.C-K. Huang thank the Ministry of Education in Taiwan, and the Cambridge Overseas Trust for funding his PhD.This is the accepted manuscript. The final version is available from the Royal Society at http://rsif.royalsocietypublishing.org/content/12/102/20141064

Dynamic modelling reveals the separable contributions to achieving correct spindle orientation in a noisy system

The mechanisms by which the mammalian mitotic spindle is guided to a predefined orientation through microtubule-cortex interactions have recently received considerable interest, but there has been no dynamic model that describes spindle movements toward the preferred axis in human cells. Here, we develop a dynamic model based on stochastic activity of cues anisotropically positioned around the cortex of the mitotic cell and we show that the mitotic spindle does not reach equilibrium before chromosome segregation. Our model successfully captures the characteristic experimental behavior of noisy spindle rotation dynamics in human epithelial cells, including a weak underlying bias in the direction of rotation, suppression of motion close to the alignment axis, and the effect of the aspect ratio of the interphase cell shape in defining the final alignment axis. We predict that the force exerted per cue has a value that minimizes the deviation of the spindle from the predefined axis. The model has allowed us to systematically explore the parameter space around experimentally relevant configurations, and predict the mechanistic function of a number of established regulators of spindle orientation, highlighting how physical modeling of a noisy system can lead to functional biological understanding. We provide key insights into measurable parameters in live cells that can help distinguish between mechanisms of microtubule and cortical-cue interactions that jointly control the final orientation of the spindle.This work was supported by Cancer Research UKThis is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.bpj.2015.08.01

Structure of Spherulites in Insulin, β-Lactoglobulin, and Amyloid β

Under denaturing conditions such as low pH and elevated temperatures, proteins in vitro can misfold and aggregate to form long rigid rods called amyloid fibrils; further self-assembly can lead to larger structures termed spherulites. Both of these aggregates resemble amyloid tangles and plaques associated with Alzheimer’s disease in vivo. The ability to form such aggregates in a multitude of different proteins suggests that it is a generic ability in their mechanism to form. Little is known about the structure of these large spherulites ranging from 5 to 100 microns and whether they can reproducibly form in amyloid β (1-40) (Aβ40), a 40-amino acid residue peptide, which is one of the major components of Alzheimer’s amyloid deposits. Here, we show that spherulites can readily form in Aβ40 under certain monomerization and denaturing conditions. Using polarized and nonpolarized Raman spectroscopy, we analyzed the secondary structure of spherulites formed from three different proteins: insulin, β-lactoglobulin (BLG), and Aβ40. Visually, these spherulites have a characteristic “Maltese Cross” structure under crossed polarizers through an optical microscope. However, our results indicate that insulin and Aβ40 spherulites have similar core structures consisting mostly of random coils with radiating fibrils, whereas BLG mostly contains β-sheets and fibrils that are likely to be spiraling from the core to the edge

A micro-incubator for cell and tissue imaging

International audienceA low-cost micro-incubator for the imaging of dynamic processes in living cells and tissues has been developed. This micro-incubator provides a tunable environment which can be altered to study the response of cell monolayers for several days as well as relatively thick tissue samples and tissue engineered epithelial tissues in experiments lasting several hours. Samples within the incubator are contained in a sterile cavity closed by a gas permeable membrane. The incubator can be positioned in any direction and used on an inverted as well as on an upright microscope. The temperature is regulated with a Peltier system controlled with a sensor positioned close to the sample to be able to compensate for any changes in temperature. Rapid changes in the environment can be applied to the sample because of the fast response of the Peltier system and the sample's adaptations to induced changes in the environment can be monitored. To evaluate the performance of the micro-incubator we report on studies using cultured cells in monolayers, on monolayers of cells stretched to breaking point on a distensible membrane, on cells in open 3D fibrous scaffolds and on fluorescently labelled polymersome penetration into 3D tissue engineered oral mucosa

Observation of the Early Structural Changes Leading to the Formation of Protein Superstructures.

Formation of superstructures in protein aggregation processes has been indicated as a general pathway for several proteins, possibly playing a role in human pathologies. There is a severe lack of knowledge on the origin of such species in terms of both mechanisms of formation and structural features. We use equine lysozyme as a model protein, and by combining spectroscopic techniques and microscopy with X-ray fiber diffraction and ab initio modeling of Small Angle X-ray Scattering data, we isolate the partially unfolded state from which one of these superstructures (i.e., particulate) originates. We reveal the low-resolution structure of the unfolded state and its mechanism of formation, highlighting the physicochemical features and the possible pathway of formation of the particulate structure. Our findings provide a novel detailed knowledge of such a general and alternative aggregation pathway for proteins, this being crucial for a basic and broader understanding of the aggregation phenomena.This is the author's accepted manuscript and will be under embargo until the 3rd of September 2015. The final version is published by ACS in The Journal of Physical Chemistry Letters here: http://pubs.acs.org/doi/abs/10.1021/jz501614e

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Levelling the playing field: maternity leave, paternity leave and the REF

For many academics, balancing research life and family life is a great challenge, and one which has not always been adequately taken account of by research assessments. Professor Athene Donald considers the initial recommendations regarding maternity leave in the REF, and welcomes the most recent HEFCE statement on this important issue