Promoting lab culture to enhance academic resilience during crises

The COVID‐19 pandemic has heavily impacted academics’ professional and personal lives, forcing many research groups (labs) to shift from an academic system primarily based on in‐person work to an almost full‐time remote workforce during lockdowns. Labs are generally characterized by a strong lab culture that underpins all research and social activities of its members. Lab culture traditionally builds on the pillars of in‐person communication, knowledge sharing, and all social and professional activities that promote collaboration, team building, scientific productivity, and well‐being. Here, we use the experience of our research group facing the COVID‐19 pandemic to illustrate how proactively reinforcing lab culture and its positive outcomes have been essential to our lab when transitioning from an in‐person to a remote lab environment, and through its ongoing evolution toward a hybrid remote/in‐person model. We argue that the proactive promotion of lab culture in research groups can foster academic resilience during crises, helping research groups to maintain their capacity to conduct scientific activities while preserving a sustainable life/work balance and a healthy mental condition.     

Numerical and Experimental Research on Modular Oscillating Fin

Fishes are famous for their ability to position themselves accurately even in turbulent flows. This ability is the result of the coordinated movement of fins which extend from the body. We have embarked on a research program designed to develop an agile and high efficient biologically inspired robotic fish based on the performance of hybrid mechanical fms. To accomplish this goal, a mechanical ray-like fin actuated by Shape Memory Alloy （SMA） is developed, which can realize both oscillatory locomotion and undulatory locomotion. We first give a brief introduction on the mechanical structure of our fin and then carry out theoretic analysis on force generation. Detailed information of these theoretical results is later revealed by Computational Huid Dynamic （CFD）, and is final validated by experiments. This robotic fin has potential application as a propulsor for future underwater vehicles in addition to being a valuable scientific instrument.     

Divergence at neutral and non-neutral loci in Drosophila buzzatii populations and their hybrids

The impact of intraspecific hybridisation on fitness and morphological traits depends on the history of natural selection and genetic drift, which may have led to differently coadapted gene-complexes in the parental populations. The divergence at neutral and non-neutral loci between populations can be evaluated by estimating F_ST and Q_ST respectively, and hence give an estimate of drift and selection in the populations. Here we investigate (1) whether divergence between populations in quantitative traits (wing size and shape) can be attributed to selection or drift alone, (2) The impact of intraspecific hybridisation on estimators for divergence at neutral (F_ST) and non-neutral loci (Q_ST) in hybrids, (3) If measurement of shape is more informative than size in order to detect divergence in quantitative traits between populations. The aims were addressed by performing two hybridisations between three populations of Drosophila buzzatii, one between populations from Argentina and the Canary Islands (separated for 200 years), and the other between populations from Argentina and Australia (separated for 80 years). We observed the highest divergence at neutral loci between the Argentinean and Canary Island populations, but highest morphological divergence between the Argentinean and Australian populations, indicating that natural selection is acting on the wings. Divergence based on Q_ST measures in the hybrids was sensitive towards increased phenotypic variance (σ²p) within groups and should be used with care when σ²p of populations differ. Our results indicate that measures of shape give a better estimate of divergence at the underlying quantitative traits loci than measures of size.     

Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype

Hypoxia-induced intrauterine growth restriction increases the risk for cardiovascular, renal, and other chronic diseases in adults, representing thus a major public health problem. Still, not much is known about the fetal mechanisms that predispose these individuals to disease. Using a previously validated mouse model of fetal hypoxia and bottom-up proteomics, we characterize the response of the fetal kidney to chronic hypoxic stress. Fetal kidneys exhibit a dichotomous response to chronic hypoxia, comprising on the one hand cellular adaptations that promote survival (glycolysis, autophagy, and reduced DNA and protein synthesis), but on the other processes that induce a senescence-like phenotype (infiltration of inflammatory cells, DNA damage, and reduced proliferation). Importantly, chronic hypoxia also reduces the expression of the antiaging proteins klotho and Sirt6, a mechanism that is evolutionary conserved between mice and humans. Taken together, we uncover that predetermined aging during fetal development is a key event in chronic hypoxia, establishing a solid foundation for Barker’s hypothesis of fetal programming of adult diseases. This phenotype is associated with a characteristic biomarker profile in tissue and serum samples, exploitable for detecting and targeting accelerated aging in chronic hypoxic human diseases.     

Otoliths as natural tags in the systematics of salmonids

Synopsis We studied otolith shape in two species of Salmo and two species of Salvelinus to quantify the accuracy of intraspecific, interspecific, and intergeneric identification. Otolith shape is chiefly population and species specific. Between genera, only 3% of the specimens were incorrectly grouped using discriminant analysis.     

A method for the generation of small pre-determined deletions in plasmid DNA: deletion analysis of the tetR region of vector pBR322

A general method is described that allows precise deletion of a chosen restriction fragment(s) from a plasmid having many cleavage sites for that restriction enzyme. The DNA to be deleted is first separated from the rest of the plasmid on a larger DNA fragment contained between two different unique restriction sites. This fragment is then subdigested by the restriction endonuclease of interest, which recognises two or more tetranucleotide (cohesive end or blunt end) sequences on the fragment, and is recloned between the two original unique restriction sites. The method is rapid, efficient, and the results are predictable. Examples are given in which predetermined HpaII (9 bp, 147 bp), TaqI (141 bp) and AluI (15 bp, 403 bp) fragments have been selectively removed from the tetR region of plasmid pBR322.     

Crown profile of foliage area characterized with the Weibull distribution in a hinoki (Chamaecyparis obtusa) stand

Summary Thirten sample trees of various sizes in a 29-year-old hinoki [Chamaecyparis obtusa (Sieb, et Zucc.) Endl.] plantation were felled and subjected to the stratified clip technique. Crown profile of foliage area fitted well with the Weibull distribution. The crown profile tended to be more skewed toward the top of crowns in smaller trees than in larger trees. This tendency was reflected in the value of the shape parameter of the Weibull distribution. The shape parameter ranged from 1.73 to 3.23 and gradually increased up to an asymptotic value with an increase of stem diameter at breast height. The scale parameter of the distribution ranged from 1.0 to 4.2 and tended to increase in proportion to stem diameter at breast height. Foliage area of a tree correlated well with stem diameter at breast height through an ordinary allometric equation. Tree height could be approximated fairly well by a generalized allometric equation as a function of stem diameter at breast height. On the basis of the census of stem diameter at breast height, canopy profile could be constructed synthesizing crown profiles of foliage area for individual trees in the stand. Leaf area index was estimated to be 6.6 ha ha^–1.     

Analysis and visualization of growth-related and treatment-induced craniofacial changes

An analysis and visualization of craniofacial shape changes due to growth or orthodontic treatment is presented. The suggested method is based on an adapted Karhunen-Loève decomposition of time-discrete data based on landmarks in lateral X-rays of the skull. It allows for a reduction of the high-dimensional dynamic problem to a few spatial modes representing synchronous components of growth patterns with time-dependent mode coefficients. The growth-related shape changes as well as the orthodontic treatment effects are visualized by overdrawing the underlying shape changes. The results based on this technique give insight into the still controversially discussed question to which degree the craniofacial skeletal structures can be influenced by orthodontic appliances.     

Effect of accounting for interfractional CTV shape variations in PTV margins on prostate cancer radiation treatment plans

PurposeThe aim of this study was to account for interfractional clinical target volume (CTV) shape variation and apply this to the planning target volume (PTV) margin for prostate cancer radiation treatment plans.MethodsInterfractional CTV shape variations were estimated from weekly cone-beam computed tomography (CBCT) images using statistical point distribution models. The interfractional CTV shape variation was taken into account in the van Herk’s margin formula. The PTV margins without and with the CTV shape variation, i.e., standard (PTV_ori) and new (PTV_shape) margins, were applied to 10 clinical cases that had weekly CBCT images acquired during their treatment sessions. Each patient was replanned for low-, intermediate-, and high-risk CTVs, using both margins. The dose indices (D98 and V70) of treatment plans with the two margins were compared on weekly pseudo-planning computed tomography (PCT) images, which were defined as PCT images registered using a deformable image registration technique with weekly CBCT images, including contours of the CTV, rectum, and bladder.ResultsThe percentage of treatment fractions of patients who received CTV D98 greater than 95% of a prescribed dose increased from 80.3 (PTV_ori) to 81.8% (PTV_shape) for low-risk CTVs, 78.8 (PTV_ori) to 87.9% (PTV_shape) for intermediate-risk CTVs, and 80.3 (PTV_ori) to 87.9% (PTV_shape) for high-risk CTVs. In most cases, the dose indices of the rectum and bladder were acceptable in clinical practice.ConclusionThe results of this study suggest that interfractional CTV shape variations should be taken into account when determining PTV margins to increase CTV coverages.     

Influence of erythrocyte shape on the rate of Ca2+-induced scrambling of phosphatidylserine

Membrane-perturbing agents that cause transformation of biconcave erythrocytes into echinocytes or stomatocytes were used to investigate the influence of erythrocyte shape on the rate of Ca²⁺-induced scrambling of phospholipids. Erythrocytes were treated with a variety of lipid-soluble compounds to induce these shape changes, followed by incubation with calcium and ionomycin to activate lipid scramblase. Prothrombinase activity of the cells was used to monitor the rate of surface exposure of phosphatidylserine, which is taken as a measure of scramblase activity. Echinocytes show an enhanced rate of scrambling, whereas stomatocytes show a reduced rate, relative to normocytes. This phenomenon appears to correlate with enhanced and diminished micro-exovesicle shedding from echinocytes and stomatocytes, respectively. It is concluded that the rate of calcium-induced phosphatidylserine exposure (rate of lipid scrambling) in erythrocytes depends for a considerable part on the cells' ability to form microvesicles.