Salvage brachytherapy for second ipsilateral breast tumor event: Relating dosimetric analysis to late side effects.

PURPOSE: For second ipsilateral breast tumor event (2ndIBTE), conservative treatment (CT) involving wide local excision plus accelerated partial breast reirradiation (APBrI) is increasingly used as an alternative to mastectomy. This study investigates the impact of APBrI technique and multicatheter interstitial high dose-rate brachytherapy (MIB) dosimetry parameters on toxicity and survival in patients with 2ndIBTE. MATERIALS-METHODS: Data from patients with 2ndIBTE treated with CT, were analyzed. Inclusion criteria specified 2ndIBTE occurring at least one year after 1st CT for primary breast cancer. Treatment details and dosimetry parameters were recorded. Primary endpoint was late toxicity. Secondary endpoints were late toxicity prognostic factors analysis and oncological outcome. RESULTS: From 07/2005 and 07/2023, 201 patients (pts) received 2nd CT. With a median follow-up of 49.6 months (44.9-59.5), tumor size was less than 2 cm (88.1%), with estrogen receptor positive (92.7%). Patients were low (63.7%) or intermediate (29.8%) GEC-ESTRO APBI risk classification. Late toxicities were observed in 34.8% (G1 52.3%, G2 40.7%). Cutaneous fibrosis was the most common toxicity. Cosmetic outcomes were excellent in 64.1%. Dosimetry analysis revealed positive correlations between complications and absolute volumes of CTV, V100, V150, and V200. Volumes requiring higher needle number and lower DNR resulted in fewer complications. 5-year disease-free and overall survival were 88% and 95% respectively. CONCLUSION: Second CT for 2ndIBTE showed favorable oncological outcomes and survival rates. Complications were correlated with specific dosimetric parameters, emphasizing the importance of tailored treatment planning. This study provides valuable insights in risk stratification and MIB optimization for APBrI.

Workflow optimization of brachytherapy-based very accelerated partial breast irradiation.

PURPOSE: For low-risk breast cancer, accelerated partial breast irradiation (APBI) is a level 1 evidence procedure. Brachytherapy based very APBI (vAPBI) makes it possible to perform adjuvant irradiation in 4 to 1 fraction. However, vAPBI organization is critical. The aim of this technical note is to report on its optimization. METHODS AND MATERIALS: To offer to low-risk breast cancer patient an efficient, simple, rapid adjuvant irradiation with a reduced number of hospital visits, a new organization of vAPBI based on a single fraction was established, merging all the different steps (from first consultation to irradiation) into a 4-5-consecutive-hour period. This therapeutic program was developed in strong collaboration with radiation oncologists, medical physicists, radiation therapists, and the medical secretary. RESULTS: After the validation of adjuvant breast irradiation, the patient was offered a telemedicine consultation with the radiation oncologist. Then, the day of vAPBI, the patient arrived at the brachytherapy unit at 08:00 AM for an in-person consultation followed by a preimplant CT scan (defining catheter number and position). After breast local anesthesia, catheter placement was performed followed by a postimplant CT scan for planning purposes. A total dose of 16 Gy in 1 fraction was delivered before removing the catheters. The patient was discharged from the brachytherapy unit around 12:30 PM with an upcoming surveillance consultation date. CONCLUSIONS: VAPBI organization optimization makes it possible to propose a short 5-h procedure from medical consultation to treatment with only one round trip. Strict organization among staff is required.

Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly.

Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, whereas highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used Drosophila suzukii as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural D. suzukii populations collected from cherry, strawberry, and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.

Single fraction of HDR brachytherapy for prostate cancer: Results of the SiFEPI phase II prospective trial.

Purpose: To report the results of the Single Fraction Early Prostate Irradiation (SiFEPI) phase 2 prospective trial. Materials/Methods: The SiFEPI trial (NCT02104362) evaluated a single fraction of high-dose rate brachytherapy (HDB) for low- (LR) and favorable-intermediate (FIR) risk prostate cancers. After rectal spacer placement, a single fraction of 20 Gy was delivered to the prostate. Oncological outcome (biochemical (bRFS) and local (lRFS) relapses, disease-free (DFS) and overall (OS) survivals and toxicity (acute/late genito-urinary (GU), gastro-intestinal (GI) and sexual (S) toxicities were investigated. Results: From 03/2014 to 10/2017, 35 pts were enrolled, of whom 33 were evaluable. With a median age of 66 y [46-79], 25 (76 %) and 8 (24 %) pts were LR and FIR respectively. With a MFU of 72.8 months [64-86], 6y-bRFS, lRFS and mRFS were 62 % [45-85], 61 % [44-85] and 93 % [85-100] respectively while 6y-DFS, CSS and OS were 54 % [37-77], 100 % and 89 % [77-100] respectively. Late GU, GI and S toxicities were observed in 11 pts (33 %;18G1), 4 pts (12 %;4G1) and 7 pts (21 %;1G1,5G2,1G3) respectively. Biochemical relapse (BR) was observed in 11 pts (33 %;7LR,4FIR) with a median time interval between HDB and BR of 51 months [24-69]. Nine of these pts (82 %) presented a histologically proven isolated local recurrence. Conclusions: Long-term results of the SiFEPI trial show that a single fraction of 20 Gy leads to sub-optimal biochemical control for LR/FIR prostate cancers. The late GU and GI toxicity profile is encouraging, leading to consideration of HDB as a safe irradiation technique.

TRPM7 Modulates Human Pancreatic Stellate Cell Activation.

Pancreatic diseases, such as pancreatitis or pancreatic ductal adenocarcinoma, are characterized by the presence of activated pancreatic stellate cells (PSCs). These cells represent key actors in the tumor stroma, as they actively participate in disease development and progression: reprograming these PSCs into a quiescent phenotype has even been proposed as a promising strategy for restoring the hallmarks of a healthy pancreas. Since TRPM7 channels have been shown to regulate hepatic stellate cells proliferation and survival, we aimed to study the role of these magnesium channels in PSC activation and proliferation. PS-1 cells (isolated from a healthy pancreas) were used as a model of healthy PSCs: quiescence or activation were induced using all-trans retinoic acid or conditioned media of pancreatic cancer cells, respectively. The role of TRPM7 was studied by RNA silencing or by pharmacological inhibition. TRPM7 expression was found to be correlated with the activation status of PS-1 cells. TRPM7 expression was able to regulate proliferation through modulation of cell cycle regulators and most importantly p53, via the PI3K/Akt pathway, in a magnesium-dependent manner. Finally, the analysis of TCGA database showed the overexpression of TRPM7 in cancer-associated fibroblasts. Taken together, we provide strong evidences that TRPM7 can be considered as a marker of activated PSCs.

High-dose-rate brachytherapy boost for elderly patients with intermediate to high-risk prostate cancer: 5-year clinical outcome of the PROSTAGE cohort.

Purpose: To analyze the oncological outcome in elderly (>70 years) prostate cancer after high-dose rate brachytherapy (HDB) boost. Materials/methods: In this retrospective study, patients with intermediate (IR) and high-risk (HR) prostate cancer underwent external beam radiation therapy (EBRT) followed by HDB boost with/without androgen deprivation therapy (ADT). The impact of age (≤70y vs. > 70y) was investigated. Oncological outcome focused on biochemical relapse-free survival (bRFS), cause-specific (CSS) and overall survival (OS). Late genito-urinary (GU) and gastro-intestinal (GI) toxicities were investigated. Results: From 07/08 to 01/22, 518 pts received a HDB boost, and 380 were analyzed (≤70y:177pts [46.6%] vs. > 70y:203pts [53.4%]). Regarding NCCN classification, 98 pts (≤70y: 53pts; >70y: 45pts; p = 0.107) and 282 pts (≤70y: 124pts; >70y: 158pts; p = NS) were IR and HR pts respectively. Median EBRT dose was 46 Gy [37.5-46] in 23 fractions [14-25]. HDB boost delivered a single fraction of 14/15 Gy (79%). ADT was used in 302 pts (≤70y: 130pts; >70y: 172pts; p = 0.01). With MFU of 72.6 months [67-83] for the whole cohort, 5-y bRFS, 5-y CSS and 5-y OS were 88% [85-92], 99% [97-100] and 94% [92-97] respectively; there was no statistical difference between the two age groups except for 5-y CSS (p = 0.05). Late GU and GI toxicity rates were 32.4% (G ≥ 3 7.3%) and 10.1% (no G3) respectively. Conclusions: For IR and HR prostate cancers, HDB boost leads to high rates of disease control with few late G ≥ 3 GU/GI toxicities. For elderly pts, HDB boost remains warranted mainly in HR pts, while competing comorbidity factors influence OS.

A hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors.

Inbreeding results from the mating of related individuals and has negative consequences because it brings together deleterious variants in one individual. Genomic estimates of the inbreeding coefficients are preferred to pedigree-based estimators as they measure the realized inbreeding levels and they are more robust to pedigree errors. Several methods identifying homozygous-by-descent (HBD) segments with hidden Markov models (HMM) have been recently developed and are particularly valuable when the information is degraded or heterogeneous (e.g., low-fold sequencing, low marker density, heterogeneous genotype quality or variable marker spacing). We previously developed a multiple HBD class HMM where HBD segments are classified in different groups based on their length (e.g., recent versus old HBD segments) but we recently observed that for high inbreeding levels with many HBD segments, the estimated contributions might be biased towards more recent classes (i.e., associated with large HBD segments) although the overall estimated level of inbreeding remained unbiased. We herein propose a new model in which the HBD classification is modelled in successive nested levels with decreasing expected HBD segment lengths, the underlying exponential rates being directly related to the number of generations to the common ancestor. The non-HBD classes are now modelled as a mixture of HBD segments from later generations and shorter non-HBD segments (i.e., both with higher rates). The new model has improved statistical properties and performs better on simulated data compared to our previous version. We also show that the parameters of the model are easier to interpret and that the model is more robust to the choice of the number of classes. Overall, the new model results in an improved partitioning of inbreeding in different HBD classes and should be preferred.

The Pharmacological and Structural Basis of the AahII-NaV1.5 Interaction and Modulation by the Anti-AahII Nb10 Nanobody.

Scorpion α-toxins are neurotoxins that target the fast inactivation mechanism of voltage-gated sodium (NaV) channels leading to several neuro- and cardiotoxic effects in mammals. The toxin AahII is the most active α-toxin from the North African scorpion Androctonus australis Hector that slows the fast inactivation of NaV channels. To fight scorpion envenomation, an anti-AahII nanobody named NbAahII10 (Nb10) was developed. The efficiency of this nanobody has been evaluated in vivo on mice, but its mechanism of action at the cellular level remains unknown. Here we have shown that AahII toxin slows the fast inactivation of the adult cardiac NaV1.5 channels, expressed in HEK293 cells, in a dose-dependent manner, while current amplitude was not affected. The inactivation of NaV1.5 is slower by a factor of 4, 7, and 35 in the presence of [AahII] at 75, 150, and 300 nM, respectively. The washout partially reversed the toxin effect on inactivation from 8.3 ± 0.9 ms to 5.2 ± 1.2 ms at 75 nM. We have also demonstrated that the highly neutralizing Nb10 can fully reverse the effect of AahII toxin on the channel inactivation kinetics even at the 1:1 M ratio. However, the 1:0.5 M ratio is not able to neutralize completely the AahII effect. Therefore, the application of Nb10 promotes a partial abolishment of AahII action. Bioinformatic analysis and prediction of NaV1.5-driven docking with AahII show that Ala39 and Arg62 of AahII play a crucial role to establish a stable interaction through H-bound interactions with Gln1615 and Lys1616 (S3-S4 extracellular loop) and Asp1553 (S1-S2 loop) from the voltage-sensing domain IV (VSD4) of NaV1.5, respectively. From this, we notice that AahII shares the same contact surface with Nb10. This strongly suggests that Nb10 dynamically replaces AahII toxin from its binding site on the NaV1.5 channel. At the physiopathological level, Nb10 completely neutralized the enhancement of breast cancer cell invasion induced by AahII. In summary, for the first time, we made an electrophysiological and structural characterization of the neutralization potent of Nb10 against the α-scorpion toxin AahII in a cellular model overexpressing NaV1.5 channels.

The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean.

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data.

Analysis of population genetic data often includes a search for genomic regions with signs of recent positive selection. One of such approaches involves the concept of extended haplotype homozygosity (EHH) and its associated statistics. These statistics typically require phased haplotypes, and some of them necessitate polarized variants. Here, we unify and extend previously proposed modifications to loosen these requirements. We compare the modified versions with the original ones by measuring the false discovery rate in simulated whole-genome scans and by quantifying the overlap of inferred candidate regions in empirical data. We find that phasing information is indispensable for accurate estimation of within-population statistics (for all but very large samples) and of cross-population statistics for small samples. Ancestry information, in contrast, is of lesser importance for both types of statistic. Our publicly available R package rehh incorporates the modified statistics presented here.

Fate of phosphorus from treated wastewater in soil-based constructed wetlands.

In France, soil-based constructed wetlands for the discharge of treated wastewater have become a popular technique to both reduce flow to surface receiving water bodies and perform complementary treatments. This study focuses on the fate of phosphorus in three different soils, as well as its assimilation by Phragmites australis. The experimental set-up consisted of three lysimeters containing three soils selected to be representative of those typically found near wastewater treatment plants (i.e. a silt loam Fluvisol, a sandy loam Fluvisol and a sandy-clay loam Technosol). Lysimeters are undisturbed soil monoliths (1.5 m3 in volume), whose masses are continuously monitored in order to obtain an accurate water mass balance. The lysimeters here were intermittently fed for 3.5 days and then left to rest for 3.5 days. The experiment lasted 26 months, including 18 months of feeding with phosphorus (PO4-P, TP) fluxes in and out being monitored along with water content, oxygen content and redox potential at various depths. The quantities of phosphorus stored in the soils and assimilated in the Phragmites australis were measured. Phosphorus fractionation in soils was performed to better understand its distribution and potential remobilization. Low phosphate concentrations were measured at the outlets of all three lysimeters, thereby highlighting satisfactory phosphorus retention in the three soils (removal efficiencies >90%). A significant amount of phosphorus can be exported by harvesting Phragmites australis aerial parts (26%, 17% and 13% of the yearly incoming phosphorus mass for the silt loam Fluvisol, sandy loam Fluvisol and sandy-clay loam Technosol, respectively). The fractionation step served to determine that the phosphorus retained in the soil was primarily bound to iron oxides/hydroxides, calcium and clay. Moreover, it was found to be preferable to hold oxidizing (aerobic) conditions and pH close to neutral in order to maintain conditions under which the complexes formed with phosphorus remain stable.

High-dose-rate brachytherapy boost for locally advanced cervical cancer: Oncological outcome and toxicity analysis of 4 fractionation schemes.

PURPOSE: Brachytherapy (BT) boost after radio-chemotherapy (RCT) is a standard of care in the management of locally advanced cervical cancer (LACC). As there is no consensus on high-dose-rate (HDR) BT fractionation schemes, our aim was to report the oncological outcome and toxicity profile of four different schemes using twice-a-day (BID) HDR-BT. PATIENTS AND METHODS: This was an observational, retrospective, single institution study for patients with LACC receiving a HDR-BT boost. The latter was performed with a single implant and single imaging done on day 1. The different fractionation schemes were: 7 Gy + 4x3.5 Gy (group 1); 7 Gy + 4x4.5 Gy (group 2); 3x7Gy (group 3) and 3x8Gy (group 4). Local (LFS), nodal (NFS) and metastatic (MFS) recurrence-free survival as well as progression-free survival (PFS) and overall survival (OS) were analyzed. Acute (≤6 months) and late toxicities (>6 months) were reported. RESULTS: From 2007 to 2018, 191 patients were included. Median follow-up was 57 months [45-132] and median EQD210D90CTVHR was 84, 82 and 90 Gy for groups 2, 3 and 4 respectively (dosimetric data missing for group 1). The 5-year LFS, NFS, MFS, PFS and OS were 85% [81-90], 83% [79-86], 70% [67-73], 61% [57-64] and 75% [69-78] respectively, with no significant difference between the groups. EQD210D90CTVHR < 85 Gy was a prognostic factor for local recurrence in univariate analysis (p = 0.045). The rates of acute/late grade ≥ 2 urinary, digestive and gynecological toxicities were 9%/15%, 3%/15% and 9%/25% respectively. CONCLUSION: Bi-fractionated HDR-BT boost seems feasible with good oncological outcome and slightly more toxicity after dose escalation.

Effect of trickling filter on carbon and nitrogen removal in vertical flow treatment wetlands: A full-scale investigation.

Vertical Flow Treatment Wetland (VF-TW) systems achieve high efficiencies in terms of carbon related parameters removals from domestic wastewaters. Nitrogen removal is also efficient but optimisations are still needed. This article reports and discusses experimental data collected from 24-h monitoring campaigns of 29 full-scale VF-TWs, having different configurations and operation time up to 13 years. All monitored systems gathered 1 or 2 stage(s) of unsaturated or partially saturated VF-TW. Additionally, some of those included an aerobic biological Tricking Filter (TF) prior to TW stage(s). Results firstly showed that the implementation of a TF improved TSS, COD and BOD5 removal rates in the monitored systems. Regarding nitrogen removal, the association of TF with one stage of partially saturated vertical TW was found to achieve around 79% of nitrification in average and up to 92% in some cases. In the configurations where TF was associated to 2 successive stages of TW, almost all total nitrogen removal by nitrification/denitrification was achieved at the outlet of the first-stage TW. The contribution of the second-stage TW in denitrification was found very low due to limited availability of organic carbon to support heterotrophic denitrification. Specific solutions to enhance the contribution of the second stage in the denitrification process are discussed.

f-Statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat.

By capturing various patterns of the structuring of genetic variation across populations, f -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariances of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the F (and D ) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq data and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) F 4 -ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving relatively low sequencing coverages. We further analysed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii, which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.

Brachytherapy for oligometastatic prostate cancer to the penis.

The origin of penile metastases is in 70% of cases from primary pelvic cancers (genitourinary and recto-sigmoid primary tumors). The prognosis is poor and it is often associated with synchronous bone metastases at the time of diagnosis. We present the case of a 61-year-old patient who developed a penile induration 7 years after radical prostatectomy followed by adjuvant external beam radiation therapy for high-risk prostatic adenocarcinoma. Biopsies confirmed the metastatic localization and a detailed assessment failed to find any further remote lesions. Faced with this penile oligometastatic prostate cancer, we proposed an ablative treatment based on interstitial multi-catheter high-dose rate brachytherapy. At the six-month follow-up, clinical examination and 68Ga-PSMA-11-PET confirmed a complete response of the penile tumor without new lesion at a distance.

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae).

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase phylogenetic information for higher-level relationships, we targeted conserved regions and assembled paired reads into long loci to enable the retrieval of homologous loci in outgroup genomes. We compared morphological and molecular results to highlight discrepancies and reveal possible inference bias. For the first time, we recovered a monophyletic subgenus Urostigma (stranglers) and a clade with all gynodioecious Ficus. However, we show, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference. Four competing positions for the root of the molecular tree are possible. The placement of section Pharmacosycea as sister to other fig trees is not supported by morphological data and considered a result of a long-branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides Ficus into monoecious versus gynodioecious species appears most plausible. It seems most likely that the ancestor of fig trees was a freestanding tree and active pollination is inferred as the ancestral state, contrary to previous hypotheses. However, ambiguity remains on the ancestral breeding system. Despite morphological plasticity, we advocate restoring a central role to morphology in our understanding of the evolution of Ficus, as it can help detect systematic errors that appear more pronounced with larger molecular datasets.

Orai1 Channel Regulates Human-Activated Pancreatic Stellate Cell Proliferation and TGFß1 Secretion through the AKT Signaling Pathway.

Activated pancreatic stellate cells (aPSCs), the crucial mediator of pancreatic desmoplasia, are characterized, among others, by high proliferative potential and abundant transforming growth factor ß1 (TGFß1) secretion. Over the past years, the involvement of Ca2+ channels in PSC pathophysiology has attracted great interest in pancreatic cancer research. We, thus, aimed to investigate the role of the Orai1 Ca2+ channel in these two PSC activation processes. Using the siRNA approach, we invalided Orai1 expression and assessed the channel functionality by Ca2+ imaging, the effect on aPSC proliferation, and TGFß1 secretion. We demonstrated the functional expression of the Orai1 channel in human aPSCs and its implication in the store-operated Ca2+ entry (SOCE). Orai1 silencing led to a decrease in aPSC proliferation, TGFß1 secretion, and AKT activation. Interestingly, TGFß1 induced a higher SOCE response by increasing Orai1 mRNAs and proteins and promoted both AKT phosphorylation and cell proliferation, abolished by Orai1 silencing. Together, our results highlight the role of Orai1-mediated Ca2+ entry in human aPSC pathophysiology by controlling cell proliferation and TGFß1 secretion through the AKT signaling pathway. Moreover, we showed a TGFß1-induced autocrine positive feedback loop by promoting the Orai1/AKT-dependent proliferation via the stimulation of Orai1 expression and function.

Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments.

The process of local adaptation involves differential changes in fitness over time across different environments. Although experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analysed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.

Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest.

Simulation-based methods such as approximate Bayesian computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. Random Forest allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated data sets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user-friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo-observed and real data sets corresponding to pool-sequencing and individual-sequencing SNP data sets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP data sets to make inferences about complex population genetic histories.