Unraveling the Evolutionary Diet Mismatch and Its Contribution to the Deterioration of Body Composition.

Over the millennia, patterns of food consumption have changed; however, foods were always whole foods. Ultra-processed foods (UPFs) have been a very recent development and have become the primary food source for many people. The purpose of this review is to propose the hypothesis that, forsaking the evolutionary dietary environment, and its complex milieu of compounds resulting in an extensive metabolome, contributes to chronic disease in modern humans. This evolutionary metabolome may have contributed to the success of early hominins. This hypothesis is based on the following assumptions: (1) whole foods promote health, (2) essential nutrients cannot explain all the benefits of whole foods, (3) UPFs are much lower in phytonutrients and other compounds compared to whole foods, and (4) evolutionary diets contributed to a more diverse metabolome. Evidence will be presented to support this hypothesis. Nutrition is a matter of systems biology, and investigating the evolutionary metabolome, as compared to the metabolome of modern humans, will help elucidate the hidden connections between diet and health. The effect of the diet on the metabolome may also help shape future dietary guidelines, and help define healthy foods.

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

Potential nutritional and functional matters in yeast culture prepared by soybean meal fermentation.

BACKGROUND: Yeast culture (YC) is a product fermented on a specific medium, which is a type of postbiotic of anaerobic solid-state fermentation. Although YC has positive effects on the animal growth and health, it contains a variety of beneficial metabolites as dark matter, which have not been quantified. In the present study, liquid chromatography-tandem mass spectrometry is employed to identify the unknown metabolites. Following their identification, the important chemicals are quantified using HPLC-diode array detection methods. RESULTS: Non-targeted metabolomics studies showed that 670 metabolites in total were identified in YC, of which 23 metabolites significantly increased, including organic acids, amino acids, nucleosides and purines, isoflavones, and other substances. The chemical quantitative analysis showed that the contents of succinic acid, aminobutyric acid, glutamine, purine and daidzein increased by 84.42%, 51.07%, 100%, 68.85% and 4.60%, respectively. CONCLUSION: Therefore, the use of non-targeted metabolomics combined with chemical quantitative analysis to reveal the nutritional and functional substances of YC could help to elucidate the postbiotic mechanism and provide theoretical support for the regulation of the directional accumulation of beneficial metabolites. © 2024 Society of Chemical Industry.

Dominance of transposable element-related satDNAs results in great complexity of "satDNA library" and invokes the extension towards "repetitive DNA library".

Research on bivalves is fast-growing, including genome-wide analyses and genome sequencing. Several characteristics qualify oysters as a valuable model to explore repetitive DNA sequences and their genome organization. Here we characterize the satellitomes of five species in the family Ostreidae (Crassostrea angulata, C. virginica, C. hongkongensis, C. ariakensis, Ostrea edulis), revealing a substantial number of satellite DNAs (satDNAs) per genome (ranging between 33 and 61) and peculiarities in the composition of their satellitomes. Numerous satDNAs were either associated to or derived from transposable elements, displaying a scarcity of transposable element-unrelated satDNAs in these genomes. Due to the non-conventional satellitome constitution and dominance of Helitron-associated satDNAs, comparative satellitomics demanded more in-depth analyses than standardly employed. Comparative analyses (including C. gigas, the first bivalve species with a defined satellitome) revealed that 13 satDNAs occur in all six oyster genomes, with Cg170/HindIII satDNA being the most abundant in all of them. Evaluating the "satDNA library model" highlighted the necessity to adjust this term when studying tandem repeat evolution in organisms with such satellitomes. When repetitive sequences with potential variation in the organizational form and repeat-type affiliation are examined across related species, the introduction of the terms "TE library" and "repetitive DNA library" becomes essential. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-024-00218-0.

The Hunt for Chemical Dark Matter across a River-to-Ocean Continuum.

Thousands of mass peaks emerge during molecular characterization of natural dissolved organic matter (DOM) using ultrahigh-resolution mass spectrometry. While mass peaks assigned to certain molecular formulas have been extensively studied, the uncharacterized mass peaks that represent a significant fraction of organic matter and convey biogenic elements and energy have been previously ignored. In this study, we introduce the term dark DOM (DDOM) for unassigned mass peaks and have explored its characteristics and environmental behaviors using a data set of 38 DOM extracts covering the Yangtze River-to-ocean continuum. We identified a total of 9141 DDOM molecules, which exhibited higher molecular weight and greater diversity than the DOM subset with assigned DOM formulas. Although DDOM contributed a smaller fraction of relative abundance, it significantly impacted the molecular weight and molecular composition of bulk DOM. A portion of DDOM with higher molecular weight was found to increase molecular abundance across the river-to-ocean continuum. These compounds could contain halogenated organic molecules and might have a high potential to contribute to the refractory organic carbon pool. With this study, we underline the contribution of dark matter to the total DOM pool and emphasize that more DDOM research is needed to understand its contribution to global biogeochemical cycles and carbon sequestration.

Dark Matter and Mirror World.

Overwhelming astronomical evidence for dark matter and absence of any laboratory evidence for it despite many dedicated searches have fueled speculation that dark matter may reside in a parallel universe interacting with the familiar universe only via gravitational interactions as well as possibly via some ultra-weak forces. In this scenario, we postulate that the visible universe co-exists with a mirror world consisting of an identical duplicate of forces and matter of our world, obeying a mirror symmetry. This picture, motivated by particle physics considerations, not only provides a natural candidate for dark matter but also has the potential to explain the matter dark matter coincidence problem, i.e., why the dark matter content of the universe is only a few times the visible matter content. One requirement for mirror models is that the mirror world must be colder than our world to maintain the success of big bang nucleosynthesis. After a review of the basic features of the model, we present several new results: first is that the consistency between the coldness of the mirror world and the explanation of the matter dark matter coincidence implies an upper bound on the inflation reheat temperature of the universe to be around 106.5 GeV. We also argue that the coldness implies the mirror world consists mainly of mirror Helium and very little mirror hydrogen, which is the exact opposite of what we see in the visible world.

Cosmic mysteries and the hydrogen 21-cm line: bridging the gap with lunar observations.

The hydrogen 21-cm signal is predicted to be the richest probe of the young Universe, including those eras known as the cosmic Dark Ages, the Cosmic Dawn (when the first star and black hole formed) and the Epoch of Reionization. This signal holds the key to deciphering processes that take place at the early stages of cosmic history. In this opinion piece, we discuss the potential scientific merit of lunar observations of the 21-cm signal and their advantages over more affordable terrestrial efforts. The Moon is a prime location for radio cosmology which will enable precision observations of the low-frequency radio sky. The uniqueness of such observations is that they will provide an unparalleled opportunity to test cosmology and the nature of dark matter using the Dark Ages 21-cm signal. No less enticing is the opportunity to obtain a much clearer picture of the Cosmic Dawn than that currently achievable from the ground, which will allow us to determine the properties of the first stars and black holes. This article is part of a discussion meeting issue 'Astronomy from the Moon: the next decades (part 2)'.

Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.

Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies. IMPORTANCE: Wastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.

Mirror QCD phase transition as the origin of the nanohertz Stochastic Gravitational-Wave Background.

Several Pulsar Timing Array (PTA) Collaborations have recently provided strong evidence for a nHz Stochastic Gravitational-Wave Background (SGWB). Here we investigate the implications of a first-order phase transition occurring within the early Universe's dark quantum chromodynamics epoch, specifically within the framework of the mirror twin Higgs dark sector model. Our analysis indicates a distinguishable SGWB signal originating from this phase transition, which can explain the measurements obtained by PTAs. Remarkably, a significant portion of the parameter space for the SGWB signal also effectively resolves the existing tensions in both the H0 and S8 measurements in Cosmology. This intriguing correlation suggests a possible common origin of these three phenomena for 0.2<ΔNeff<0.5, where the mirror dark matter component constitutes less than 30% of the total dark matter abundance. Next-generation CMB experiments such as CMB-S4 can test this parameter region.

Further understanding the interaction between dark energy and dark matter: current status and future directions.

The interaction between dark matter and dark energy (DE) can be incorporated into field theory models of DE that have proved successful in alleviating the coincidence problem. We review recent advances in this field, including new models and constraints from different astronomical data sets. We show that interactions are allowed by observations and can reduce the current tensions among different measurements of cosmological parameters. We extend our discussion to include constraints from non-linear effects and results from cosmological simulations. Finally, we discuss forthcoming multi-messenger data from current and future observational facilities that will help to improve our understanding of the interactions within the dark sector.

Community characterization of soil from the Central Deccan Plateau dry tropical deciduous forest (Ceddtrof) in central India using 16S rRNA gene amplicon sequencing.

We report a preliminary study of soil from the Central Deccan Plateau dry tropical deciduous forest in India using 16S rRNA gene amplicon sequencing. We report diverse taxa, e.g., Proteobacteria, Actinobacteria, Acidobacteria, Plactomycetes, Chloroflexi, Bacteroidetes, Verrucomicrobia, Gemmatimonadetes, Firmicutes, Crenarchaeota, Nitrospirae, Armatimonadetes, Elusimicrobia, Cyanobacteria, Chlamydiae, Chlorobi, Parvachaeota, Tenericutes, Euryarchaeota, Fibrobacteres, Calditrix, and Spirochaetes.

Rare event searches with cryogenic detectors.

Cryogenic detectors can detect the smallest energy depositions via the scattering of the incoming particle with the detector material. The deposited energy leads to minimal temperature rises of a few [Formula: see text], read out via transition edge sensors and SQUIDs. Using scintillating crystals as detector material offers the possibility of discriminating between nuclear recoils from dark matter scattering and electromagnetic background events. The CRESST experiment pioneered this technology and is still among the most sensitive experiments searching for sub-GeV dark matter particles. The technology is now also used by other experiments for dark matter searches (COSINUS) and for measuring coherent elastic neutrino-nucleus scattering (NUCLEUS). We discuss cryogenic detectors' detection principle and their application. We present the latest dark matter results from CRESST, a new type of background, and the status of the COSINUS and NUCLEUS experiments. This article is part of the theme issue 'The particle-gravity frontier'.

The cosmological constant and scale hierarchies with emergent gauge symmetries.

Motivated by the stability of the electroweak Higgs vacuum we consider the possibility that the Standard Model might work up to large scales between about [Formula: see text] GeV and close to the Planck scale. A plausible scenario is an emergent Standard Model with gauge symmetries originating in some topological-like phase transition deep in the ultraviolet. In this case, the cosmological constant scale and neutrino masses should be of similar size, suppressed by factor of the large scale of emergence. The key physics involves a subtle interplay of Poincaré invariance, mass generation and renormalization group invariance. The Higgs mass would be environmentally selected in connection with vacuum stability. Consequences for dark matter scenarios are discussed. This article is part of the theme issue 'The particle-gravity frontier'.

Dual-phase xenon time projection chambers for rare-event searches.

In the past decade, dual-phase xenon time projection chambers (Xe-TPCs) have emerged as some of the most powerful detectors in the fields of astroparticle physics and rare-event searches. Developed primarily towards the direct detection of dark matter particles, experiments presently operating deep underground have reached target masses at the multi-tonne scale, energy thresholds of approximately 1 keV and radioactivity-induced background rates similar to those from solar neutrinos. These unique properties, together with demonstrated stable operation over several years, allow for the exploration of new territory via high-sensitivity searches for a plethora of ultra-rare interactions. These include searches for particle dark matter, for second-order weak decays, and the observation of astrophysical neutrinos. We first review some properties of xenon as a radiation detection medium and the operation principles of dual-phase Xe-TPCs together with their energy calibration and resolution. We then discuss the status of currently running experiments and of proposed next-generation projects, describing some of the technological challenges. We end by looking at their sensitivity to dark matter candidates, to second-order weak decays and to solar and supernova neutrinos. Experiments based on dual-phase Xe-TPCs are difficult and, like all good experiments, they are constantly pushed to their limits. Together with many other endeavours in astroparticle physics and cosmology they will continue to push at the borders of the unknown, hopefully to reveal profound new knowledge about our cosmos. This article is part of the theme issue 'The particle-gravity frontier'.

Higgs-induced screening mechanisms in scalar-tensor theories.

We consider the theory of a light conformally coupled scalar field, that is, one that is coupled directly to the Ricci scalar of the gravitational sector. This theory can be written equivalently as one of a light scalar that is coupled to the Standard Model of particle physics with a particular combination of Higgs-portal couplings. When the conformal coupling function contains terms that are linear and quadratic in the conformally coupled scalar, we find that the effective mass of the light propagating mode and its coupling to matter fields, obtained after expanding around a minimum of the classical potential, depend on the energy density of the background environment. This is despite the absence of nonlinear terms in the original equation of motion for the light conformally coupled field. Instead, we find that the nonlinearities of the prototype Higgs potential are communicated to the light mode. In this way, we present a novel realization of screening mechanisms, in which light degrees of freedom coupled to the Standard Model are able to avoid experimental constraints through environmental and thin-shell effects.

Application of culturomics in fungal isolation from mangrove sediments.

BACKGROUND: Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties. RESULTS: This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1). CONCLUSIONS: Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.

Constraints on Tsallis Cosmology from Big Bang Nucleosynthesis and the Relic Abundance of Cold Dark Matter Particles.

By employing Tsallis' extensive but non-additive δ-entropy, we formulate the first two laws of thermodynamics for gravitating systems. By invoking Carathéodory's principle, we pay particular attention to the integrating factor for the heat one-form. We show that the latter factorizes into the product of thermal and entropic parts, where the entropic part cannot be reduced to a constant, as is the case in conventional thermodynamics, due to the non-additive nature of Sδ. The ensuing two laws of thermodynamics imply a Tsallis cosmology, which is then applied to a radiation-dominated universe to address the Big Bang nucleosynthesis and the relic abundance of cold dark matter particles. It is demonstrated that the Tsallis cosmology with the scaling exponent δ∼1.499 (or equivalently, the anomalous dimension Δ∼0.0013) consistently describes both the abundance of cold dark matter particles and the formation of primordial light elements, such as deuterium 2H and helium 4He. Salient issues, including the zeroth law of thermodynamics for the δ-entropy and the lithium 7Li problem, are also briefly discussed.

Evidence for widespread existence of functional novel and non-canonical human transcripts.

BACKGROUND: Fraction of functional sequence in the human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches. RESULTS: In this work, we established a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool in aneuploid cells. Application of this approach to human cell lines in multiple phenotypic screens suggested the presence of many yet uncharacterized functional elements in the human genome, represented at least in part by novel exons of known and novel genes. The novel transcripts containing these exons can be massively, up to thousands-fold, induced by specific stresses, and at least some can represent bi-cistronic protein-coding mRNAs. CONCLUSIONS: Altogether, these results argue that many unannotated and non-canonical human transcripts, including those that appear as aberrant splice products, have biological relevance under specific biological conditions.

Implications of nano-Hertz gravitational waves on electroweak phase transition in the singlet dark matter model.

Inspired by the recent evidences of nano-Hertz stochastic gravitational waves observed by the pulsar timing array collaborations, we explore their implied supercooled electroweak phase transition in the singlet extension of the standard model. Our findings reveal that by adjusting the model parameter at per milli level, the corresponding percolation temperature can be continuously lowered to 1 GeV. With such a low percolation temperature, the singlet dark matter may freeze out before the electroweak phase transition, and, consequently, the entropy generated during the transition can significantly affect the dark matter relic density. It alleviates the tension between the requirement of a strong electroweak phase transition and the constraints imposed by dark matter direct detection, and can be tested in future experiments.