Specialized replication mechanisms maintain genome stability at human centromeres.

The high incidence of whole-arm chromosome aneuploidy and translocations in tumors suggests instability of centromeres, unique loci built on repetitive sequences and essential for chromosome separation. The causes behind this fragility and the mechanisms preserving centromere integrity remain elusive. We show that replication stress, hallmark of pre-cancerous lesions, promotes centromeric breakage in mitosis, due to spindle forces and endonuclease activities. Mechanistically, we unveil unique dynamics of the centromeric replisome distinct from the rest of the genome. Locus-specific proteomics identifies specialized DNA replication and repair proteins at centromeres, highlighting them as difficult-to-replicate regions. The translesion synthesis pathway, along with other factors, acts to sustain centromere replication and integrity. Prolonged stress causes centromeric alterations like ruptures and translocations, as observed in ovarian cancer models experiencing replication stress. This study provides unprecedented insights into centromere replication and integrity, proposing mechanistic insights into the origins of centromere alterations leading to abnormal cancerous karyotypes.

Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging.

Sanguina nivaloides is the main alga forming red snowfields in high mountains and Polar Regions. It is non-cultivable. Analysis of environmental samples by X-ray tomography, focused-ion-beam scanning-electron-microscopy, physicochemical and physiological characterization reveal adaptive traits accounting for algal capacity to reside in snow. Cysts populate liquid water at the periphery of ice, are photosynthetically active, can survive for months, and are sensitive to freezing. They harbor a wrinkled plasma membrane expanding the interface with environment. Ionomic analysis supports a cell efflux of K+, and assimilation of phosphorus. Glycerolipidomic analysis confirms a phosphate limitation. The chloroplast contains thylakoids oriented in all directions, fixes carbon in a central pyrenoid and produces starch in peripheral protuberances. Analysis of cells kept in the dark shows that starch is a short-term carbon storage. The biogenesis of cytosolic droplets shows that they are loaded with triacylglycerol and carotenoids for long-term carbon storage and protection against oxidative stress.

Unraveling the optical shape of snow.

The reflection of sunlight off the snow is a major driver of the Earth's climate. This reflection is governed by the shape and arrangement of ice crystals at the micrometer scale, called snow microstructure. However, snow optical models overlook the complexity of this microstructure by using simple shapes, and mainly spheres. The use of these various shapes leads to large uncertainties in climate modeling, which could reach 1.2 K in global air temperature. Here, we accurately simulate light propagation in three-dimensional images of natural snow at the micrometer scale, revealing the optical shape of snow. This optical shape is neither spherical nor close to the other idealized shapes commonly used in models. Instead, it more closely approximates a collection of convex particles without symmetry. Besides providing a more realistic representation of snow in the visible and near-infrared spectral region (400 to 1400 nm), this breakthrough can be directly used in climate models, reducing by 3 the uncertainties in global air temperature related to the optical shape of snow.

Short-term molecular consequences of chromosome mis-segregation for genome stability.

Chromosome instability (CIN) is the most common form of genome instability and is a hallmark of cancer. CIN invariably leads to aneuploidy, a state of karyotype imbalance. Here, we show that aneuploidy can also trigger CIN. We found that aneuploid cells experience DNA replication stress in their first S-phase and precipitate in a state of continuous CIN. This generates a repertoire of genetically diverse cells with structural chromosomal abnormalities that can either continue proliferating or stop dividing. Cycling aneuploid cells display lower karyotype complexity compared to the arrested ones and increased expression of DNA repair signatures. Interestingly, the same signatures are upregulated in highly-proliferative cancer cells, which might enable them to proliferate despite the disadvantage conferred by aneuploidy-induced CIN. Altogether, our study reveals the short-term origins of CIN following aneuploidy and indicates the aneuploid state of cancer cells as a point mutation-independent source of genome instability, providing an explanation for aneuploidy occurrence in tumors.

Dispensers for pheromonal pest control.

The detrimental effects of pesticides on the environment and human health have motivated the development of alternative pest control strategies. Pheromonal pest control is one alternative strategy that is attractive because most pheromones used commercially are non-toxic. Pheromones are also effective at low concentrations, and insects are slower to develop resistance to them compared to pesticides. Pheromones can be used to control pests by attracting them towards traps, repelling them from crops, or disrupting their mating behaviour. Viability of pheromonal control strategies must be evaluated on a case-by-case basis and depends on the target species, the pheromone being used, the specific control strategy, the method of dispensing pheromone, other pest control strategies pheromones being used alongside, and many other factors. The efficacy of pheromonal control has been demonstrated in commercial applications such as the control of palm weevils using traps releasing their male aggregation pheromone. Mating disruption using female sex pheromones has also been widely applied for control of both the codling moth Cydia Pomonella and the european grapevine moth Lobesia Botrana (Bangels and Beliën, 2012; Lucchi et al., 2018). Pheromones are volatiles that both degrade quickly in the environment and can be rapidly dispersed by wind. Consequently, administering pheromones to fields requires the use of dispensers that emits pheromone continuously or intermittently. Septum dispensers, membrane dispensers and solid matrix dispensers are best suited to treating smaller areas of cropland since they need to be installed by hand, a labor-intensive process. For treating a large area with pheromones, sprayable formulations and aerosol dispensers are alternative dispensing technologies that can be employed. The characteristics of these different dispenser designs are discussed as well as the kinetics governing pheromone release. Possible areas for future work in pheromone dispenser technology include examining new integrated strategies that employ pheromones alongside other pest control techniques in unique ways. The combination of pheromonal control with physical exclusion or predator release are examples of integrated strategies that are promising but have yet to be widely commercialized. Most commercial pheromonal dispensers are also noted to be impossible or impractical to reuse, apart from aerosol devices. Creating new types of rechargeable dispenser might have some cost saving benefits and would be an interesting area for future innovation in this field.

Identification of several eating habits that mediate the association between eating behaviors and the risk of obesity.

Objective: Eating behaviors play important roles in the development of obesity. A better knowledge of the psychological aspects of eating behaviors in individuals with and without obesity and their consequences on daily eating and lifestyle habits would be informative. The Three-Factor Eating Questionnaire (TFEQ)-R21 assesses the psychometrics of eating behavior. The objectives of the study were to establish which eating habits were or were not associated with TFEQ eating behaviors, and to quantify the extent to which those eating habits mediated the association between TFEQ eating behaviors and obesity risk. Methods: Data were obtained from the Gene and Environment Case-Control Obesity Study from northern France. It included 2237 individuals with obesity and 403 individuals without obesity. Eating behaviors were assessed according to the TFEQ-R21. Two activity levels (physical activity and television watching) and six eating habits (e.g., plate size, having one serving or at least two servings of the main meal, …) were evaluated. Regression and mediation analyses were performed. Results: Higher cognitive restraint, higher uncontrolled eating (UE) and higher emotional eating (EE) were associated with a higher risk of obesity, independently of each other and of age, sex, socio-economic status and physical activity. Cognitive restraint was negatively associated with having at least two servings, while UE and EE were associated with several obesogenic habits such as eating in front of the television or eating at night. Each of these obesogenic habits mediated between 3% and 20% of the association between UE or EE and obesity. Conclusions: Psychological eating behaviors were associated with several lifestyle and eating habits in both individuals with and without obesity. Moreover, some eating habits partially mediated (between 3% and 20%) the association between TFEQ eating behaviors and obesity risk. For clinicians, this study shows that simple, easy-to-ask questions on specific daily eating habits can provide essential information to better understand and manage patients with obesity.

Black carbon and dust alter the response of mountain snow cover under climate change.

By darkening the snow surface, mineral dust and black carbon (BC) deposition enhances snowmelt and triggers numerous feedbacks. Assessments of their long-term impact at the regional scale are still largely missing despite the environmental and socio-economic implications of snow cover changes. Here we show, using numerical simulations, that dust and BC deposition advanced snowmelt by 17 ± 6 days on average in the French Alps and the Pyrenees over the 1979-2018 period. BC and dust also advanced by 10-15 days the peak melt water runoff, a substantial effect on the timing of water resources availability. We also demonstrate that the decrease in BC deposition since the 1980s moderates the impact of current warming on snow cover decline. Hence, accounting for changes in light-absorbing particles deposition is required to improve the accuracy of snow cover reanalyses and climate projections, that are crucial for better understanding the past and future evolution of mountain social-ecological systems.

Semisynthetic transformation of banana peel to enhance the conversion of sugars to 5-hydroxymethylfurfural.

This study aimed to efficiently convert banana peels (BP) into 5-hydroxymethylfurfural (HMF) by using an integrated mechanoenzymatic/catalytic approach. There is no report on HMF production using mechanoenzymatic hydrolysis. Moreover, this method enables saccharification of lignocellulose without bulk solvents or pretreatment. The effects of the reaction volume, milling time, and reactive aging (RAging) on the mechanoenzymatic hydrolysis of BP were studied. The solvent-free enzymatic hydrolysis of BP under RAging conditions was found to provide higher glucose (40.5 wt%) and fructose (17.2 wt%) yields than chemical hydrolysis. Next, the conversion of the resulting monosaccharides into HMF in the presence of the AlCl3·H2O/HCl-DMSO/H2O system resulted in 71.9 mol% yield, which is so far the highest HMF yield obtained from cellulosic food wastes. Under identical reaction conditions, direct conversion of untreated BP to HMF yielded 22.7 mol% HMF, suggesting that mechanoenzymatic hydrolysis greatly promotes the release of sugars from BP to improve HMF yield.

Solid-state co-culture fermentation of simulated food waste with filamentous fungi for production of bio-pigments.

The use of waste stream residues as feedstock for material production simultaneously helps reduce dependence on fossil-based resources and to shift toward a circular economy. This study explores the conversion of food waste into valuable chemicals, namely, bio-pigments. Here, a simulated food waste feedstock was converted into pigments via solid-state fermentation with the filamentous fungus Talaromyces albobiverticillius (NRRL 2120). Pigments including monascorubrin, rubropunctatin, and 7-(2-hydroxyethyl)-monascorubramine were identified as products of the fermentation via ultra-performance liquid chromatography coupled with quadrupole-time-of-flight electrospray ionization mass spectrometry. Pigments were obtained at concentrations of 32.5, 20.9, and 22.4 AU/gram dry substrate for pigments absorbing at 400, 475, and 500 nm, respectively. Pigment production was further enhanced by co-culturing T. albobiverticillius with Trichoderma reesei (NRRL 3652), and ultimately yielded 63.8, 35.6, and 43.6 AU/gds at the same respective wavelengths. This represents the highest reported production of pigments via solid-state fermentation of a non-supplemented waste stream feedstock. KEY POINTS: • Simulated food waste underwent solid-state fermentation via filamentous fungi. • Bio-pigments were obtained from fermentation of the simulated food waste. • Co-culturing multiple fungal species substantially improved pigment production.

Kronos scRT: a uniform framework for single-cell replication timing analysis.

Mammalian genomes are replicated in a cell type-specific order and in coordination with transcription and chromatin organization. Currently, single-cell replication studies require individual processing of sorted cells, yielding a limited number (<100) of cells. Here, we develop Kronos scRT, a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform or cell sorting, which allows investigating large datasets obtained from asynchronous cells. By applying our tool to published data as well as droplet-based single-cell whole-genome sequencing data generated in this study, we exploit scRT from thousands of cells for different mouse and human cell lines. Our results demonstrate that although genomic regions are frequently replicated around their population average RT, replication can occur stochastically throughout S phase. Altogether, Kronos scRT allows fast and comprehensive investigations of the RT programme at the single-cell resolution for both homogeneous and heterogeneous cell populations.

Development of a Nuclear Magnetic Resonance Method and a Near Infrared Calibration Model for the Rapid Determination of Lipid Content in the Field Pea (Pisum sativum).

Pisum sativum is a leguminous crop suitable for cultivation worldwide. It is used as a forage or dried seed supplement in animal feed and, more recently, as a potential non-traditional oilseed. This study aimed to develop a low-cost, rapid, and non-destructive method for analyzing pea lipids with no chemical modifications that would prove superior to existing destructive solvent extraction methods. Different pea accession seed samples, prepared as either small portions (0.5 mm2) of endosperm or ground pea seed powder for comparison, were subjected to HR-MAS NMR analyses and whole seed samples underwent NIR analyses. The total lipid content ranged between 0.57-3.45% and 1.3-2.6% with NMR and NIR, respectively. Compared to traditional extraction with butanol, hexane-isopropanol, and petroleum ether, correlation coefficients were 0.77 (R2 = 0.60), 0.56 (R2 = 0.47), and 0.78 (R2 = 0.62), respectively. Correlation coefficients for NMR compared to traditional extraction increased to 0.97 (R2 = 0.99) with appropriate correction factors. PLS regression analyses confirmed the application of this technology for rapid lipid content determination, with trends fitting models often close to an R2 of 0.95. A better robust NIR quantification model can be developed by increasing the number of samples with more diversity.

CENP-B-mediated DNA loops regulate activity and stability of human centromeres.

Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.

Valorization of Spent Coffee Grounds as Precursors for Biopolymers and Composite Production.

Spent coffee grounds (SCG) are a current subject in many works since coffee is the second most consumed beverage worldwide; however, coffee generates a high amount of waste (SCG) and can cause environmental problems if not discarded properly. Therefore, several studies on SCG valorization have been published, highlighting its waste as a valuable resource for different applications, such as biofuel, energy, biopolymer precursors, and composite production. This review provides an overview of the works using SCG as biopolymer precursors and for polymer composite production. SCG are rich in carbohydrates, lipids, proteins, and minerals. In particular, carbohydrates (polysaccharides) can be extracted and fermented to synthesize lactic acid, succinic acid, or polyhydroxyalkanoate (PHA). On the other hand, it is possible to extract the coffee oil and to synthesize PHA from lipids. Moreover, SCG have been successfully used as a filler for composite production using different polymer matrices. The results show the reasonable mechanical, thermal, and rheological properties of SCG to support their applications, from food packaging to the automotive industry.

Use of filamentous fungi as biocatalysts in the oxidation of 5-(hydroxymethyl)furfural (HMF).

The objective of this study was to explore the use of filamentous fungi as oxidative biocatalysts. To that end, filamentous fungal whole-cells, comprising five different species were employed in the oxidation of 5-(hydroxymethyl)furfural (HMF). Two species (A. niger and T. reesei), which demonstrated superior HMF conversion and product accumulation, were further evaluated for growth on alternative substrates (e.g. pentoses) as well as for use in a chemo-biocatalytic reaction system. Concerning the latter, the two whole-cell biocatalysts were coupled with laccase/TEMPO in a one-pot reaction designed to enable catalysis of the three oxidative steps necessary to convert HMF into 2,5-furandicarboxylic acid (FDCA), a compound with immense potential in the production of sustainable and eco-friendly polymers. Ultimately, the optimal one-pot chemo-biocatalytic cascade system, comprising 1 g/L T. reesei whole cells coupled with 2.5 mM laccase and 20 mol% TEMPO, achieved a molar yield of 88% after 80 h.

Gene copy-number changes and chromosomal instability induced by aneuploidy confer resistance to chemotherapy.

Mitotic errors lead to aneuploidy, a condition of karyotype imbalance, frequently found in cancer cells. Alterations in chromosome copy number induce a wide variety of cellular stresses, including genome instability. Here, we show that cancer cells might exploit aneuploidy-induced genome instability and the resulting gene copy-number changes to survive under conditions of selective pressure, such as chemotherapy. Resistance to chemotherapeutic drugs was dictated by the acquisition of recurrent karyotypes, indicating that gene dosage might play a role in driving chemoresistance. Thus, our study establishes a causal link between aneuploidy-driven changes in gene copy number and chemoresistance and might explain why some chemotherapies fail to succeed.

CENP-A overexpression promotes distinct fates in human cells, depending on p53 status.

Tumour evolution is driven by both genetic and epigenetic changes. CENP-A, the centromeric histone H3 variant, is an epigenetic mark that directly perturbs genetic stability and chromatin when overexpressed. Although CENP-A overexpression is a common feature of many cancers, how this impacts cell fate and response to therapy remains unclear. Here, we established a tunable system of inducible and reversible CENP-A overexpression combined with a switch in p53 status in human cell lines. Through clonogenic survival assays, single-cell RNA-sequencing and cell trajectory analysis, we uncover the tumour suppressor p53 as a key determinant of how CENP-A impacts cell state, cell identity and therapeutic response. If p53 is functional, CENP-A overexpression promotes senescence and radiosensitivity. Surprisingly, when we inactivate p53, CENP-A overexpression instead promotes epithelial-mesenchymal transition, an essential process in mammalian development but also a precursor for tumour cell invasion and metastasis. Thus, we uncover an unanticipated function of CENP-A overexpression to promote cell fate reprogramming, with important implications for development and tumour evolution.

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy.

Chromosome segregation relies on centromeres, yet their repetitive DNA is often prone to aberrant rearrangements under pathological conditions. Factors that maintain centromere integrity to prevent centromere-associated chromosome translocations are unknown. Here, we demonstrate the importance of the centromere-specific histone H3 variant CENP-A in safeguarding DNA replication of alpha-satellite repeats to prevent structural aneuploidy. Rapid removal of CENP-A in S phase, but not other cell-cycle stages, caused accumulation of R loops with increased centromeric transcripts, and interfered with replication fork progression. Replication without CENP-A causes recombination at alpha-satellites in an R loop-dependent manner, unfinished replication, and anaphase bridges. In turn, chromosome breakage and translocations arise specifically at centromeric regions. Our findings provide insights into how specialized centromeric chromatin maintains the integrity of transcribed noncoding repetitive DNA during S phase.

Induction of spontaneous human neocentromere formation and long-term maturation.

Human centromeres form primarily on α-satellite DNA but sporadically arise de novo at naive ectopic loci, creating neocentromeres. Centromere inheritance is driven primarily by chromatin containing the histone H3 variant CENP-A. Here, we report a chromosome engineering system for neocentromere formation in human cells and characterize the first experimentally induced human neocentromere at a naive locus. The spontaneously formed neocentromere spans a gene-poor 100-kb domain enriched in histone H3 lysine 9 trimethylated (H3K9me3). Long-read sequencing revealed this neocentromere was formed by purely epigenetic means and assembly of a functional kinetochore correlated with CENP-A seeding, eviction of H3K9me3 and local accumulation of mitotic cohesin and RNA polymerase II. At formation, the young neocentromere showed markedly reduced chromosomal passenger complex (CPC) occupancy and poor sister chromatin cohesion. However, long-term tracking revealed increased CPC assembly and low-level transcription providing evidence for centromere maturation over time.

Centromere strength: just a sense of proportion.

The overall structure and composition of human centromeres have been well reported, but how these elements vary between individual chromosomes and influence the chromosome-specific behavior during mitosis remains untested. In our study, we discover the existence of heterogeneity of centromeric DNA features that dictates the chromosome segregation fidelity during mitosis.

A genetic memory initiates the epigenetic loop necessary to preserve centromere position.

Centromeres are built on repetitive DNA sequences (CenDNA) and a specific chromatin enriched with the histone H3 variant CENP-A, the epigenetic mark that identifies centromere position. Here, we interrogate the importance of CenDNA in centromere specification by developing a system to rapidly remove and reactivate CENP-A (CENP-AOFF/ON ). Using this system, we define the temporal cascade of events necessary to maintain centromere position. We unveil that CENP-B bound to CenDNA provides memory for maintenance on human centromeres by promoting de novo CENP-A deposition. Indeed, lack of CENP-B favors neocentromere formation under selective pressure. Occasionally, CENP-B triggers centromere re-activation initiated by CENP-C, but not CENP-A, recruitment at both ectopic and native centromeres. This is then sufficient to initiate the CENP-A-based epigenetic loop. Finally, we identify a population of CENP-A-negative, CENP-B/C-positive resting CD4+ T cells capable to re-express and reassembles CENP-A upon cell cycle entry, demonstrating the physiological importance of the genetic memory.