Loss Of Fitness Research Articles

Communities of metazoan parasites in seven sympatric skate species (Elasmobranchii, Rajidae) from the English Channel and Celtic Sea differing in conservation status

AbstractElasmobranch populations are in steep decline mainly due to overfishing bycatch, but parasites may accelerate the collapse of vulnerable and/or highly parasitized species. We therefore studied metazoan parasites of Rajidae from the northeast Atlantic: vulnerable Leucoraja fullonica, near‐threatened Raja brachyura, Raja clavata, Raja microocellata and Raja undulata, and least‐concerned Raja montagui and Leucoraja naevus. Overall prevalence varied from 19% for R. montagui to 100% for L. fullonica. Parasite communities differed between skate species, and prevalence and abundance were higher for L. fullonica, R. microocellata, and R. undulata. We recorded 11 parasite taxa in the study: three nematodes, six cestodes, one monogenean, and one myxosporean. Whatever the skate species, the parasite component community comprised at least two nematode taxa among Phocanema spp., Proleptus sp. and Anisakis simplex. DNA‐sequencing revealed that Phocanema azarasi and Phocanema krabbei both occurred in R. microocellata and R. undulata. Phocanema spp. was first recorded in L. fullonica, L. naevus, R. microocellata, R. montagui, and R. undulata, as Proleptus sp. in L. fullonica, and A. simplex in L. fullonica and R. clavata, Rockacestus sp. and Nybelinia sp. in R. undulata, and gill‐myxosporeans on L. fullonica, L. naevus, R. microocellata, and R. undulata. The occurrence of 16 new host–parasite associations suggests potential environmental changes. Information provided by trophically transmitted helminths confirmed an opportunistic skate diet based on crustaceans and fish. We discuss results in terms of host fitness loss, bioindicator role of parasites, and anisakiasis risk. We recommend incorporating parasitology in research to improve elasmobranch conservation.

Characterization of a natural 'dead-end' variant of Schmallenberg virus.

Schmallenberg virus (SBV) belongs to the Simbu serogroup within the family Peribunyaviridae, genus Orthobunyavirus and is transmitted by Culicoides biting midges. Infection of naïve ruminants in a critical phase of gestation may lead to severe congenital malformations. Sequence analysis from viremic animals revealed a very high genome stability. In contrast, sequence variations are frequently described for SBV from malformed fetuses. In addition to S segment mutations, especially within the M segment encoding the major immunogen Gc, point mutations or genomic deletions are also observed. Analysis of the SBV_D281/12 isolate from a malformed fetus revealed multiple point mutations in all three genome segments. It also has a large genomic deletion in the antigenic domain encoded by the M segment compared to the original SBV reference strain 'BH80/11' isolated from viremic blood in 2011. Interestingly, SBV_D281/12 showed a marked replication deficiency in vitro in Culicoides sonorensis cells (KC cells), but not in standard baby hamster kidney cells (BHK-21). We therefore generated a set of chimeric viruses of rSBV_D281/12 and wild-type rSBV_BH80/11 by reverse genetics, which were characterized in both KC and BHK-21 cells. It could be shown that the S segment of SBV_D281/12 is responsible for the replication deficit and that it acts independently from the large deletion within Gc. In addition, a single point mutation at position 111 (S to N) of the nucleoprotein was identified as the critical mutation. Our results suggest that virus variants found in malformed fetuses and carrying characteristic genomic mutations may have a clear 'loss of fitness' for their insect hosts in vitro. It can also be concluded that such mutations lead to virus variants that are no longer part of the natural transmission cycle between mammalian and insect hosts. Interestingly, analysis of a series of SBV sequences confirmed the S111N mutation exclusively in samples of malformed fetuses and not in blood from viremic animals. The characterization of these changes will allow the definition of protein functions that are critical for only one group of hosts.

Enhancing mitochondrial proteolysis alleviates alpha-synuclein-mediated cellular toxicity

Parkinson’s disease (PD) is a progressive neurodegenerative disease characterized by mitochondrial dysfunction and accumulation of alpha-synuclein (α-Syn)-containing protein aggregates known as Lewy bodies (LB). Here, we investigated the entry of α-Syn into mitochondria to cause mitochondrial dysfunction and loss of cellular fitness in vivo. We show that α-Syn expressed in yeast and human cells is constitutively imported into mitochondria. In a transgenic mouse model, the level of endogenous α-Syn accumulation in mitochondria of dopaminergic neurons and microglia increases with age. The imported α-Syn is degraded by conserved mitochondrial proteases, most notably NLN and PITRM1 (Prd1 and Cym1 in yeast, respectively). α-Syn in the mitochondrial matrix that is not degraded interacts with respiratory chain complexes, leading to loss of mitochondrial DNA (mtDNA), mitochondrial membrane potential and cellular fitness decline. Importantly, enhancing mitochondrial proteolysis by increasing levels of specific proteases alleviated these defects in yeast, human cells, and a PD model of mouse primary neurons. Together, our results provide a direct link between α-synuclein-mediated cellular toxicity and its import into mitochondria and reveal potential therapeutic targets for the treatment of α-synucleinopathies.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management.

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

Abstract PR014: Combinatorial genetic screens to map synthetic lethal interactions and identify new cancer drug targets in KRAS mutant cancers

Abstract The success of precision oncology depends on our ability to translate accumulating genomic data into actionable treatment options in a personalized manner. The first step requires the identification of a specific genomic signature, then matching this signature with the most effective therapy. Unfortunately, more often than not, we do not have a specific cancer drug that is effective for the mutation found in a specific tumor. We desperately need to identify new targets so that we can develop new drugs to deliver on the promise of precision cancer medicine. In addition, we need to develop a rational way to combine drugs that does not depend on trial and error. Combinatorial genetic screening CRISPR-Cas9 now allows us to identify synthetic lethal interactions in which simultaneous perturbation of two genes leads to cell death. However, multiplex gene editing to reveal these synergies between genes is a major challenge. For model systems like yeast, high-throughput methods and technologies have made it possible to create genetic networks with around 23 million double mutants (6000 genes x 6000 genes) and has resulted in the most detailed genetic interaction network to date consisting of ∼900,000 genetic interactions. This landscape of genetic interaction network of yeast has taken the scientific research community 15 years. In human cells, there are ∼20,000 genes and 400 million combinations, making this very complex network impossible to screen and test all these 400M combinations. To systematically interrogate such genetic interactions, we designed a dual CRISPR-Cas9 perturbation library targeting the top 1000 genes upregulated in KRAS mutant cancers (lung, pancreas and colon cancers). We performed these combinatorial double knockout screens on 100K (100x1000) unique gene pairs and identified 27 pairs whose co-disruption results in a loss of cellular fitness. We next validated those top synthetic lethal pairs of genes by performing secondary screens using CRISPR-Cas12a on more KRAS mutant and KRAS WT cell lines. Overall, our findings will provide insight into potential combinational targets in KRAS mutant tumors and will highlight the synthetic lethality effects that occurs among the novel targets, and other proliferation, metastasis, immune and metabolism modules. Citation Format: Rand Arafeh, Laura Chang, Lydia Sawyer, Helen Wang, James McFarland, Joshua Dempster, Peter DeWeirdt, John Doench, William C. Hahn. Combinatorial genetic screens to map synthetic lethal interactions and identify new cancer drug targets in KRAS mutant cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR014.

The use of cell and larval assays to identify target genes for RNA interference-meditated control of the Australian sheep blowfly (Lucilia cuprina).

Flystrike, primarily caused by Lucilia cuprina, is a major health and welfare issue for sheep wool industries. Current chemical-based controls can have limited effectiveness due to the emergence of resistance in the parasite. RNA interference (RNAi), which uses double-stranded RNA (dsRNA) as a trigger molecule, has been successfully investigated for the development of innovative pest control strategies. Although RNAi offers great potential, the efficient identification, selection of target genes and delivery of dsRNA represent challenges to be overcome for the successful application of RNAi for control of L. cuprina. A primary L. cuprina (blowfly) embryo cell line (BFEC) was established and confirmed as being derived from L. cuprina eggs by PCR and amplicon sequencing. The BFECs were successfully transfected with plasmids and messenger RNA (mRNA) expressing fluorescent reporter proteins and dsRNA using lipid-based transfection reagents. The transfection of dsRNA into BEFC in this study suggested decreased mRNA levels of target gene expression, which suggested RNAi-mediated knockdown. Three of the dsRNAs identified in this study resulted in reductions of in target gene mRNA levels in BFEC and loss of biological fitness by L. cuprina larvae in a feeding bioassay. This study confirms that the novel BFEC cell line can be used to improve the efficacy of dsRNA-mediated screening to accelerate the identification of potential target genes in the development of RNAi mediated control approaches for L. cuprina. The research models established in this study are encouraging with respect to the use of RNAi as a blowfly control method, however further improvement and validation are required for field applicationsnot prefect, and could be ongoing developing. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Improved mixture correntropy cubature Kalman filter for attitude estimation

Abstract This work proposes an algorithm based on improved mixture correntropy cubature Kalman filtering (IMC-CKF) to address the issues of low accuracy and susceptibility to complex noise and outlier interference in inertial navigation attitude estimation. First, a combination of Gaussian kernel and Cauchy kernel is suggested to construct mixture correntropy to tackle the problem of single kernel-based correntropy being insufficient to confronted with complex noise. Second, the model fitting loss based on mean square error and measurement fitting loss based on mixture correntropy are used to establish the objective function. The maximum correntropy criterion (MCC) replaces the minimum mean square error (MMSE) criterion, and the fixed-point iteration method is used to solve the objective function, deriving the mixture correntropy matrix to adjust the measurement noise variance. Finally, the semi-trapezoidal membership function is used to determine the mixture correntropy coefficient. Accordingly, the algorithm can adaptively select the proportions of each kernel function according to the respective noise interference situation. Simulations and dynamic–static experiments have been conducted, and the algorithm has been compared with single kernel-based correntropy algorithms and other robust algorithms to confirm its superior precision and stability under complex noise and outlier interference.

Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups

Inbreeding depression, the loss of offspring fitness due to consanguineous mating, is generally detrimental for individual performance and population viability. We investigated inbreeding effects in a declining population of Antarctic fur seals (Arctocephalus gazella) at Bird Island, South Georgia. Here, localised warming has reduced the availability of the seal’s staple diet, Antarctic krill, leading to a temporal increase in the strength of selection against inbred offspring, which are increasingly failing to recruit into the adult breeding population. However, it remains unclear whether selection operates before or after nutritional independence at weaning. We therefore used microsatellite data from 885 pups and their mothers, and SNP array data from 98 mother–offspring pairs, to quantify the effects of individual and maternal inbreeding on three important neonatal fitness traits: birth mass, survival and growth. We did not find any clear or consistent effects of offspring or maternal inbreeding on any of these traits. This suggests that selection filters inbred individuals out of the population as juveniles during the time window between weaning and recruitment. Our study brings into focus a poorly understood life-history stage and emphasises the importance of understanding the ecology and threats facing juvenile pinnipeds.

A Practical Hybrid Hysteresis Model for Calculating Iron Core Losses in Soft Magnetic Materials

Accurately calculating the losses of ferromagnetic materials is crucial for optimizing the design and ensuring the safe operation of electrical equipment such as motors and power transformers. Commonly used loss calculation models include the Bertotti empirical formula and hysteresis models. In this paper, a new hybrid hysteresis model method is proposed to calculate losses—namely, the combination of the Jiles–Atherton hysteresis model (J–A) and the Fourier hysteresis model. The traditional Jiles–Atherton hysteresis model is mainly suitable for fitting the saturation hysteresis loop, but the fitting error is relatively large for internal minor hysteresis loops. In contrast, the Fourier hysteresis model is suitable for fitting the minor hysteresis loops because the corresponding magnetic induction strength or magnetic field is lower and the waveform distortion is small. Moreover, Fourier series expansion can be expressed with fewer terms, which is convenient for parameter fitting. Through examples, the results show that the hybrid hysteresis model can take advantage of the strengths of each model, not only reducing computational complexity, but also ensuring high fitting accuracy and loss calculation accuracy.

Virulence is associated with daily rhythms in the within-host replication of the malaria parasite Plasmodium chabaudi.

Most malaria (Plasmodium spp.) parasite species undergo asexual replication synchronously within the red blood cells of their vertebrate host. Rhythmicity in this intraerythrocytic developmental cycle (IDC) enables parasites to maximise exploitation of the host and align transmission activities with the time of day that mosquito vectors blood feed. The IDC is also responsible for the major pathologies associated with malaria, and plasticity in the parasite's rhythm can confer tolerance to antimalarial drugs. Both the severity of infection (virulence) and synchrony of the IDC vary across species and between genotypes of Plasmodium; however, this variation is poorly understood. The theory predicts that virulence and IDC synchrony are negatively correlated, and we tested this hypothesis using two closely related genotypes of the rodent malaria model Plasmodium chabaudi that differ markedly in virulence. We also test the predictions that, in response to perturbations to the timing (phase) of the IDC schedule relative to the phase of host rhythms (misalignment), the virulent parasite genotype recovers the correct phase relationship faster, incurs less fitness losses and so hosts benefit less from misalignment when infected with a virulent genotype. Our predictions are partially supported by results suggesting that the virulent parasite genotype is less synchronous in some circumstances and recovers faster from misalignment. While hosts were less anaemic when infected by misaligned parasites, the extent of this benefit did not depend on parasite virulence. Overall, our results suggest that interventions to perturb the alignment between the IDC schedule, and host rhythms and increase synchrony between parasites within each IDC, could alleviate disease symptoms. However, virulent parasites, which are better at withstanding conventional antimalarial treatment, would also be intrinsically better able to tolerate such interventions.

Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis

The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.

Detraining among Athletes-Is Withdrawal of Adaptive Cardiovascular Changes a Hint for the Differential Diagnosis of Physically Active People?

An athlete's training aims to achieve the highest possible sports results by improving physical dispositions which lead to cardiac adaptive changes. The annual training cycle is divided into periods. The preparatory period begins with gradually increasing training intensity and volume until the competitive period occurs, when the athlete's maximum performance is expected. Finally, the athlete enters a phase of loss of fitness, which is called detraining. Detraining is a time of resting both physically and mentally from the training regime and usually lasts about 4 weeks for endurance athletes. We collected data from much research on athletes' detraining. According to these data, the earliest change after detraining seems to be a decrease in left ventricular wall thickness and left ventricular mass, followed by decreased performance parameters, diastolic diameter of the left ventricle and size of the left atrium. A reversal of adaptive changes affects the left heart chamber first, then the right atrium and, finally, the right ventricle. Training reduction is often proposed as a method of differentiating an athlete's heart from cardiomyopathies. The aim of this study is to consider the diagnostic value of detraining in differentiating athletes' hearts from cardiomyopathies. We suggest that detraining cannot be conclusive in differentiating the disease from adaptive changes. Although a withdrawal of the characteristic morphological, functional and electrocardiographic changes occurs in healthy athletes during detraining, it can also concern individuals with cardiomyopathies due to the lower expression of abnormal features after decreased training loads. Therefore, a quick diagnosis and individual assessments using imaging and genetic tests are essential to recommend a proper type of activity.

FiTMuSiC: leveraging structural and (co)evolutionary data for protein fitness prediction

Systematically predicting the effects of mutations on protein fitness is essential for the understanding of genetic diseases. Indeed, predictions complement experimental efforts in analyzing how variants lead to dysfunctional proteins that in turn can cause diseases. Here we present our new fitness predictor, FiTMuSiC, which leverages structural, evolutionary and coevolutionary information. We show that FiTMuSiC predicts fitness with high accuracy despite the simplicity of its underlying model: it was among the top predictors on the hydroxymethylbilane synthase (HMBS) target of the sixth round of the Critical Assessment of Genome Interpretation challenge (CAGI6) and performs as well as much more complex deep learning models such as AlphaMissense. To further demonstrate FiTMuSiC’s robustness, we compared its predictions with in vitro activity data on HMBS, variant fitness data on human glucokinase (GCK), and variant deleteriousness data on HMBS and GCK. These analyses further confirm FiTMuSiC’s qualities and accuracy, which compare favorably with those of other predictors. Additionally, FiTMuSiC returns two scores that separately describe the functional and structural effects of the variant, thus providing mechanistic insight into why the variant leads to fitness loss or gain. We also provide an easy-to-use webserver at https://babylone.ulb.ac.be/FiTMuSiC, which is freely available for academic use and does not require any bioinformatics expertise, which simplifies the accessibility of our tool for the entire scientific community.

Recognizing interspecific dominance signals? Blue tits adjust nest defence based on great tit's black bib size

AbstractAnimals use colours, morphological structures and behaviour to advertise their dominance status and ability to obtain resources (Resource Holding Potential, RHP) in agonistic contexts with conspecifics. Dominance relationships are also known between species, although the interactions and the information used to assess the other species' RHP remain obscure and empirical evidence of interspecific recognition of status is hard to obtain. Using behavioural inference is particularly important when a species needs to assess the potential loss of fitness in terms of reproduction or survival (e.g., risk of damage or predation) that could be inflicted by another species acting as a predator, parasite or competitor. Our study shows for the first time the existence of interspecific recognition of status signals: Blue tits Cyanistes caeruleus (subordinate species) perceive Great tits Parus major (dominant species) as threats as hole‐nesting competitors, and respond differently based on the size of the great tit's black tie stripe. Blue tits seemed to recognize the meaning of great tits' black ties because they were bolder when defending their nests against small‐tie (less dominant) great tits than when repelling attacks by large‐tie (more dominant) great tit males. Our results stress that behavioural inference can potentially be used to assess the meaning of status signals that presumably evolved in an intraspecific signalling context.

Effect of Aerobic Strength Training on Physical Fitness and Weight Loss of Female University Students

There is still a growing global trend of physical inactivity despite several research showing the positive effects of exercise on health. Furthermore, the most effective weight-loss or weight-control approach is still up for debate. The literature has proven that suggested aerobic strength training (AST) enhances a variety of physical performance outcomes in sports, which helps to validate the effectiveness of AST on physical fitness and weight reduction. Even though AST is one of the most popular strength training techniques, more research is needed to fully understand how it affects female university students' ability to lose weight and perform physically. The purpose of this study was to test the impact of 8 weeks of aerobic strength exercises in female students for physical fitness and weight loss. The study sample comprised overall female students of the Islamia University of Bahawalpur (Baghdad-ul-jaded Campus). The participants of the study were (n = 30) females with ages between (M = 254.5; SD = 30.58 years) were divided into two groups: The experimental group (EG; n=15), and the control group (CG; n=15). Prior to and after the intervention, participants experienced physical and anthropometric measurements. Data were analyzed by applying descriptive, paired sample t-test, and independent t-test. Only a significant improvement for LHGS (p = 0.05), agility (p = 0.00), flexibility (p = 0.01), skipping (p = 0.01), 30-m SRT (p = 0.00) were found in all physical fitness parameters and participants significantly losing weight for the EG (p<0.05) as compared to the control group. The findings suggest that AST improves female students' physical fitness, and helps to reduce weight.

Abstract 5779: Enhancing selectivity and overcoming tissue-specific toxicity in drug discovery: A novel BET inhibitor with targeted delivery for prostate cancer treatment

Abstract Improving selectivity and circumventing tissue-specific toxicity remain significant challenges in the realm of contemporary drug discovery. Despite the advanced development of highly selective inhibitors, their systemic distribution often stimulates off-tissue unwanted side-toxicity. To address this, we engineered a highly selective inhibitor that specifically targets and releases a small molecule drug payload to a desired cell type. As a proof of concept, we apply this method to epigenetic inhibitors of BET proteins, which are crucial regulators of gene transcription implicated in the progression and survival of cancer. We engineered a novel BET-selective chemotype conjugated to a Prostate-Cancer specific targeting component in order to overcome the off-tissue effects of state-of-the-art BET inhibitors. To achieve delivery of the compound, we modified the benzodiazepine (BzD) scaffold of the well-established BET inhibitor I-BET762, conjugating the tertiary amine with a self-immolating motif, allowing for intracellular compound release upon an enzymatic trigger. This new chemotype, RT53, maintains the biochemical properties of I-BET762, showing potent and selective binding to BET bromodomains in a range of established biophysical assays. In cells, RT53 phenocopied I-BET762 on cancer cell lines, including prostate cancer. We validated the established strong anti-proliferative effect following BET inhibition using clonogenic assays, flow cytometry, and monitored the suppression of MYC expression. Moreover, we established the transcriptional rationale for loss of cellular fitness using RNA sequencing, discovering strong down-regulation of solute carriers, depriving cells of nutrient flux and disrupting normal processes. Furthermore, RT53 exhibits antitumor activity in vivo, in localized models of prostate cancer established in male athymic nude mice. The targeted delivery of RT53 demonstrated superior efficacy in vivo ameliorating on-target, off-tissue toxicity, as low-dose treatment led to almost complete elimination of grafted tumor sites, significant extension of survival, and no signs of toxicity on non-targeted tissues. Taken together, our data establish a novel class of BET-specific inhibitors offering a handle for selective delivery in vivo, enhancing the therapeutic index while avoiding on-target off-tissue toxicity. Citation Format: Cong Tang, Rui Traquete, Elizabeth Henderson, João Conde, Sara Picaud, Panagis Filippakopoulos, Gonçalo Bernardes. Enhancing selectivity and overcoming tissue-specific toxicity in drug discovery: A novel BET inhibitor with targeted delivery for prostate cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5779.

Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus.

The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.

Unsupervised Point Cloud Representation Learning by Clustering and Neural Rendering

Data augmentation has contributed to the rapid advancement of unsupervised learning on 3D point clouds. However, we argue that data augmentation is not ideal, as it requires a careful application-dependent selection of the types of augmentations to be performed, thus potentially biasing the information learned by the network during self-training. Moreover, several unsupervised methods only focus on uni-modal information, thus potentially introducing challenges in the case of sparse and textureless point clouds. To address these issues, we propose an augmentation-free unsupervised approach for point clouds, named CluRender, to learn transferable point-level features by leveraging uni-modal information for soft clustering and cross-modal information for neural rendering. Soft clustering enables self-training through a pseudo-label prediction task, where the affiliation of points to their clusters is used as a proxy under the constraint that these pseudo-labels divide the point cloud into approximate equal partitions. This allows us to formulate a clustering loss to minimize the standard cross-entropy between pseudo and predicted labels. Neural rendering generates photorealistic renderings from various viewpoints to transfer photometric cues from 2D images to the features. The consistency between rendered and real images is then measured to form a fitting loss, combined with the cross-entropy loss to self-train networks. Experiments on downstream applications, including 3D object detection, semantic segmentation, classification, part segmentation, and few-shot learning, demonstrate the effectiveness of our framework in outperforming state-of-the-art techniques.

Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells.

Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-scale CRISPR-Cas9 chemical-genetic screens in PDAC cells and found selective loss of cell fitness upon disruption of the cytidine deaminases APOBEC3C and APOBEC3D. Following gemcitabine treatment, APOBEC3C and APOBEC3D promote DNA replication stress resistance and cell survival by deaminating cytidines in the nuclear genome to ensure DNA replication fork restart and repair in PDAC cells. We provide evidence that the chemical-genetic interaction between APOBEC3C or APOBEC3D and gemcitabine is absent in nontransformed cells but is recapitulated across different PDAC cell lines, in PDAC organoids and in PDAC xenografts. Thus, we uncover roles for APOBEC3C and APOBEC3D in DNA replication stress resistance and offer plausible targets for improving gemcitabine-based therapies for PDAC.

In vitro evaluation of shape-memory hydrogels for removable dental prostheses and optimization of phase-transition temperature for intraoral use

Removable dental prostheses require periodic relining with the loss of intaglio surface fit because of mucosal shape changes over time. Therefore, a new material with high adaptability to tissue changes over time would be beneficial. This study focused on a shape-memory gel (SMG) that softens when heated, retains its shape when cooled, and returns to its original shape when reheated. The purpose was to optimize SMG for intraoral use by controlling the ratio of 2 acrylate monomers and to evaluate the changes in the shape memory and physical properties of SMG with temperature and to evaluate biocompatibility. SMG specimens were synthesized using the following mixing ratios of 2 monomers, docosyl acrylate (DA) and stearyl acrylate (SA): 0:100, 25:75, 50:50, 75:25, and 100:0. SMG specimens were photopolymerized using a fluorescent light-polymerizing unit. To evaluate shape memory as a function of temperature, permanent deformation was measured based on the standardized compression set test for thermoplastic rubber. For evaluation of the physical properties and cytotoxicity, a 3-dimensionally printed denture base material was used as the control material. All assessments were compared between the groups by using 1-way analysis of variance followed by the Tukey-Kramer multiple comparison test (α=.05). SMGs with a higher amount of DA maintained their compressed shape at room and intraoral temperatures. However, the SMG matrices softened and recovered their original shapes above 60°C. SMGs showed Shore A hardness equivalent to that of the denture-base polymer material at intraoral temperatures because of the high phase-transition temperature. The low water solubility of SMGs supported the biocompatibility test results. SMG, in which the phase-transition temperature was controlled by mixing acrylate monomers with different melting points, exhibited shape memory in the intraoral environment. The results indicate the feasibility of applying SMG for the fabrication of removable dental prostheses because of its high adaptability to tissue changes over time and biocompatibility.