An Algal Greening of Land.

Photosynthetic eukaryotes arose ∼1.5 billion years ago by endosymbiosis with a cyanobacterium. Algae then evolved for a billion years before one lineage finally colonized land. Why the wait? The Chara braunii genome details a decisive step linking plant origins with Earth's history.

Energy in Ancient Metabolism.

Modern metabolism would not work without ATP and phosphate, but in primordial biochemical networks, energy currencies might have been simpler. Goldford et al. report a novel systems approach to reconstructing energetics in ancient metabolism, with very interesting results.

Extracellular Vesicles from Trypanosoma brucei Mediate Virulence Factor Transfer and Cause Host Anemia.

Intercellular communication between parasites and with host cells provides mechanisms for parasite development, immune evasion, and disease pathology. Bloodstream African trypanosomes produce membranous nanotubes that originate from the flagellar membrane and disassociate into free extracellular vesicles (EVs). Trypanosome EVs contain several flagellar proteins that contribute to virulence, and Trypanosoma brucei rhodesiense EVs contain the serum resistance-associated protein (SRA) necessary for human infectivity. T. b. rhodesiense EVs transfer SRA to non-human infectious trypanosomes, allowing evasion of human innate immunity. Trypanosome EVs can also fuse with mammalian erythrocytes, resulting in rapid erythrocyte clearance and anemia. These data indicate that trypanosome EVs are organelles mediating non-hereditary virulence factor transfer and causing host erythrocyte remodeling, inducing anemia.

The Ribofilm as a Concept for Life's Origins.

Recent phylogenetic data indicating that the first archaea were methane-producing galvanizes cross-disciplinary evidence supporting the hypothesis that life arose via thermodynamically directed events at hydrothermal vents. The new developments lead us to propose the concept of a ribofilm in which RNA's origin-of-life role is more akin to a slowly changing platform than a spontaneous self-replicator.

The origin of membrane bioenergetics.

Harnessing energy as ion gradients across membranes is as universal as the genetic code. We leverage new insights into anaerobe metabolism to propose geochemical origins that account for the ubiquity of chemiosmotic coupling, and Na(+)/H(+) transporters in particular. Natural proton gradients acting across thin FeS walls within alkaline hydrothermal vents could drive carbon assimilation, leading to the emergence of protocells within vent pores. Protocell membranes that were initially leaky would eventually become less permeable, forcing cells dependent on natural H(+) gradients to pump Na(+) ions. Our hypothesis accounts for the Na(+)/H(+) promiscuity of bioenergetic proteins, as well as the deep divergence between bacteria and archaea.

Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation.

Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.

Autoregulatory mechanism of enzyme activity by the nuclear localization signal of lysine-specific demethylase 1.

The N-terminal region of the human lysine-specific demethylase 1 (LSD1) has no predicted structural elements, contains a nuclear localization signal (NLS), undergoes multiple posttranslational modifications (PTMs), and acts as a protein-protein interaction hub. This intrinsically disordered region (IDR) extends from core LSD1 structure, resides atop the catalytic active site, and is known to be dispensable for catalysis. Here, we show differential nucleosome binding between the full-length and an N terminus deleted LSD1 and identify that a conserved NLS and PTM containing element of the N terminus contains an alpha helical structure, and that this conserved element impacts demethylation. Enzyme assays reveal that LSD1's own electropositive NLS amino acids 107 to 120 inhibit demethylation activity on a model histone 3 lysine 4 dimethyl (H3K4me2) peptide (Kiapp âˆ¼ 3.3 µM) and histone 3 lysine 4 dimethyl nucleosome substrates (IC50 ∼ 30.4 µM), likely mimicking the histone H3 tail. Further, when the identical, inhibitory NLS region contains phosphomimetic modifications, inhibition is partially relieved. Based upon these results and biophysical data, a regulatory mechanism for the LSD1-catalyzed demethylation reaction is proposed whereby NLS-mediated autoinhibition can occur through electrostatic interactions, and be partially relieved through phosphorylation that occurs proximal to the NLS. Taken together, the results highlight a dynamic and synergistic role for PTMs, intrinsically disordered regions, and structured regions near LSD1 active site and introduces the notion that phosphorylated mediated NLS regions can function to fine-tune chromatin modifying enzyme activity.

Chemical Antiquity in Metabolism.

ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.

Edge Functionalization of Bulk γ-Graphyne Facilitates Mechanical Exfoliation and Modulates the Mode of Sheet Stacking.

We have successfully achieved selective and efficient functionalization of sheet edges in microcrystalline multilayer γ-graphyne through two methods: cross-coupling with residual bromide edge groups and copper-catalyzed azide-alkyne cycloaddition (CuAAC) with edge terminal alkyne groups. This modification significantly enhances the ease of mechanical exfoliation and dispersibility of the sheets of γ-graphyne. Specifically, C18-grafted γ-graphyne forms stable dispersions in compatible organic solvents, allowing for the imaging of atomically thin layers of γ-graphyne for the first time. Additionally, we have discovered that phenylacetylide edge groups alter the preferred stacking mode of γ-graphyne sheets. Few-layer flakes of Ph-edge γ-graphyne exhibit a preference for the R3m space group, contrasting with the aperiodic stacking of Br-edge γ-graphyne. These results open the door for scalable exfoliation of few-layer flakes of γ-graphyne with a high aspect ratio, enabling potential applications in carbon electronics.

Synthesis and biological evaluation of orally active anti-Trypanosoma agents.

In previous studies, we developed anti-trypanosome tubulin inhibitors with promising in vitro selectivity and activity against Human African Trypanosomiasis (HAT). However, for such agents, oral activity is crucial. This study focused on further optimizing these compounds to enhance their ligand efficiency, aiming to reduce bulkiness and hydrophobicity, which should improve solubility and, consequently, oral bioavailability. Using Trypanosoma brucei brucei cells as the parasite model and human normal kidney cells and mouse macrophage cells as the host model, we evaluated 30 new analogs synthesized through combinatorial chemistry. These analogs have fewer aromatic moieties and lower molecular weights than their predecessors. Several new analogs demonstrated IC50s in the low micromolar range, effectively inhibiting trypanosome cell growth without harming mammalian cells at the same concentration. We conducted a detailed structure-activity relationship (SAR) analysis and a docking study to assess the compounds' binding affinity to trypanosome tubulin homolog. The results revealed a correlation between binding energy and anti-Trypanosoma activity. Importantly, compound 7 displayed significant oral activity, effectively inhibiting trypanosome cell proliferation in mice.

Flexural properties and fatigue limit of 3D-printed and milled resin-based materials.

PURPOSE: The purpose of this study was to evaluate the flexural strength (FS), flexural modulus (FM), and fatigue limit (FL) of 3D-printed resin-based polymers and composites and compare them to 3D-printed composites. MATERIALS AND METHODS: A bar-shaped specimen (25 × 2 × 2 mm) was CAD designed according to ISO 4049:2019, and 60 duplicates of the 3D model were nested at a 45-degree angle with the printing platform and 3D-printed with three materials: denture teeth resin (Denture Teeth, Formlabs), temporary crown and bridge resin (Temporary CB, Formlabs), and composite (Flexcera Smile Ultra+, Desktop Health). The 3D model was also imported into a dental CAM software, duplicated 60 times, nested, and milled from a 3D-milled composite puck (Ivotion Denture Teeth, Ivoclar). All specimens were post-processed following the manufacturer's recommendation. The specimens were then subjected to a three-point bending test until failure using a Universal Testing Machine at a crosshead speed of 0.75 mm/min, and FS and FM were calculated. The remaining thirty specimens were tested for Fatigue Limit using the staircase approach starting at 50% FS maximum up to 1.2 M cycles at 10 Hz. The data were analyzed using one-way ANOVA and the Weibull distribution (α = 0.05). RESULTS: The results showed that Ivotion and Flexcera had higher FS (110.3 ± 7.1 MPa and 107.6 ± 6.4 MPa, respectively) and FM (3.3 ± 0.1 GPa and 3.0 ± 0.2 GPa, respectively) compared to the 3D-printed Denture Teeth (FS = 66.4 ± 18.5 MPa and FM = 1.8 ± 0.1 GPa) and Temporary CB (FS = 79.6 ± 12.1 MPa and FM = 2.7 ± 0.4 GPa). Weibull analysis showed that the Ivotion and Flexcera had a more uniform and narrower spatial distribution of defects (m: 27.98 and 29.19) than the printed materials, which had m values of 8.17 and 4.11 for Temporary CB and Denture Teeth, respectively. Although no differences were found in the static properties (FS and FM) between Ivotion and Flexcera, Ivotion presented a higher endurance limit than Flexcera (51.43 vs. 40.95 MPa). The Temporary CB presented 21.08 MPa and Denture Teeth presented 17.80 MPa of endurance limit. CONCLUSIONS: 3D-milled (Ivotion Denture Teeth) and 3D-printed (Flexcera Smile Ultra+) composites outperformed 3D-printed resins (Formlabs Denture Teeth and Temporary Crown & Bridge) in terms of flexural properties and fatigue resistance. 3D-milled (Ivotion) and 3D-printed (Flexcera) composites exhibited similar flexural properties, but 3D-milled composites showed a 25% higher fatigue endurance limit, suggesting improved clinical longevity.

Carbon-Metal Bonds: Rare and Primordial in Metabolism.

Submarine hydrothermal vents are rich in hydrogen (H2), an ancient source of electrons and chemical energy for life. Geochemical H2 stems from serpentinization, a process in which rock-bound iron reduces water to H2. Reactions involving H2 and carbon dioxide (CO2) in hydrothermal systems generate abiotic methane and formate; these reactions resemble the core energy metabolism of methanogens and acetogens. These organisms are strict anaerobic autotrophs that inhabit hydrothermal vents and harness energy via H2-dependent CO2 reduction. Serpentinization also generates native metals, which can reduce CO2 to formate and acetate in the laboratory. The enzymes that channel H2, CO2, and dinitrogen (N2) into methanogen and acetogen metabolism are the backbone of the most ancient metabolic pathways. Their active sites share carbon-metal bonds which, although rare in biology, are conserved relics of primordial biochemistry present at the origin of life.

Direct Synthesis of Formamide from CO2 and H2O with Nickel-Iron Nitride Heterostructures under Mild Hydrothermal Conditions.

Formamide can serve as a key building block for the synthesis of organic molecules relevant to premetabolic processes. Natural pathways for its synthesis from CO2 under early earth conditions are lacking. Here, we report the thermocatalytic conversion of CO2 and H2O to formate and formamide over Ni-Fe nitride heterostructures in the absence of synthetic H2 and N2 under mild hydrothermal conditions. While water molecules act as both a solvent and hydrogen source, metal nitrides serve as nitrogen sources to produce formamide in the temperature range of 25-100 °C under 5-50 bar. Longer reaction times promote the C-C bond coupling and formation of acetate and acetamide as additional products. Besides liquid products, methane and ethane are also produced as gas-phase products. Postreaction characterization of Ni-Fe nitride particles reveals structural alteration and provides insights into the potential reaction mechanism. The findings indicate that gaseous CO2 can serve as a carbon source for the formation of C-N bonds in formamide and acetamide over the Ni-Fe nitride heterostructure under simulated hydrothermal vent conditions.

Development of IFNß-1a versions with reduced immunogenicity and full in vitro biological activity for the treatment of multiple sclerosis.

IFNß (recombinant interferon Beta) has been widely used for the treatment of Multiple sclerosis for the last four decades. Despite the human origin of the IFNß sequence, IFNß is immunogenic, and unwanted immune responses in IFNß-treated patients may compromise its efficacy and safety in the clinic. In this study, we applied the DeFT (De-immunization of Functional Therapeutics) approach to producing functional, de-immunized versions of IFNß-1a. Two de-immunized versions of IFNß-1a were produced in CHO cells and designated as IFNß-1a(VAR1) and IFNß-1a(VAR2). First, the secondary and tertiary protein structures were analyzed by circular dichroism spectroscopy. Then, the variants were also tested for functionality. While IFNß-1a(VAR2) showed similar in vitro antiviral activity to the original protein, IFNß-1a(VAR1) exhibited 40% more biological potency. Finally, in vivo assays using HLA-DR transgenic mice revealed that the de-immunized variants showed a markedly reduced immunogenicity when compared to the originator.

Inhibition of RNA degradation integrates the metabolic signals induced by osmotic stress into the Arabidopsis circadian system.

The circadian clock system acts as an endogenous timing reference that coordinates many metabolic and physiological processes in plants. Previous studies have shown that the application of osmotic stress delays circadian rhythms via 3'-phospho-adenosine 5'-phosphate (PAP), a retrograde signalling metabolite that is produced in response to redox stress within organelles. PAP accumulation leads to the inhibition of exoribonucleases (XRNs), which are responsible for RNA degradation. Interestingly, we are now able to demonstrate that post-transcriptional processing is crucial for the circadian response to osmotic stress. Our data show that osmotic stress increases the stability of specific circadian RNAs, suggesting that RNA metabolism plays a vital role in circadian clock coordination during drought. Inactivation of XRN4 is sufficient to extend circadian rhythms as part of this response, with PRR7 and LWD1 identified as transcripts that are post-transcriptionally regulated to delay circadian progression.

Impact of time-restricted feeding on kidney injury in male rats with experimental metabolic syndrome.

Disruptions to circadian rhythm may be implicated in the pathogenesis of metabolic syndrome (Met-S). For example, eating during an extended period of the day may negatively impact the circadian rhythms governing metabolic control, contributing, therefore, to Met-S and associated end-organ damage. Accordingly, time-restricted eating (TRE)/feeding (TRF) is gaining popularity as a dietary intervention for the treatment and prevention of Met-S. To date, no studies have specifically examined the impact of TRE/TRF on the renal consequences of Met-S. The proposed study seeks to use a model of experimental Met-S-associated kidney disease to address this knowledge gap, disambiguating therein the effects of calorie restriction from the timing of food intake. Spontaneously hypertensive rats will consume a high-fat diet (HFD) for 8 weeks and then be allocated by stratified randomisation according to albuminuria to one of three groups. Rats will have free 24-h access to HFD (Group A), access to HFD during the scheduled hours of darkness (Group B) or access to HFD provided in the form of two rations, one provided during the light phase and one provided during the dark phase, equivalent overall in quantity to that consumed by rats in Group B (Group C). The primary outcome measure will be a change in albuminuria. Changes in food intake, body weight, blood pressure, glucose tolerance, fasting plasma insulin, urinary excretion of C-peptide and renal injury biomarkers, liver and kidney histopathology and inflammation, and fibrosis-related renal gene expression will be assessed as secondary outcomes.

Selection criteria for immediate implant placement and immediate loading for single tooth replacement in the maxillary esthetic zone: A systematic review and meta-analysis.

OBJECTIVES: The aim of this study was to review available evidence for Type 1A (immediate implant placement and immediate loading) of single tooth replacement in the maxillary esthetic zone. MATERIALS AND METHODS: An electronic search was conducted utilizing the databases of MEDLINE, Embase, and Cochrane to identify publications reporting on the outcomes of Type 1A for single tooth replacement in the maxillary esthetic zone. The success and survival rates of the included articles were reported, which were further categorized according to the clinical criteria reported in Type 1A. Mean survival rates were univariately compared between risk groups and additionally between studies published before and since 2012 using bias-corrected and study size-weighed bootstrap tests. A study time-correcting meta-analysis was then performed to obtain an overall effect for the study pool. RESULTS: A total of 3118 publications were identified in the search, with a total of 68 articles included. A mean number of implants per study were 37.2 and mean follow-up was 2.8 years. All the included studies utilizing Type 1A report highly selective inclusion and exclusion criteria. Univariate risk group comparison determined that studies before 2012 report a significantly lower mean survival rate (difference of -1.9 percentage points [PP], 95% CI: [-0.3, -4.0], p = .02), facial gap dimension had an impact on survival rates (+3.1 PP [0.2, 5.3] for width >2 mm, p = .04), as well as presence of endodontic infection (+2.6 PP [0.9, 5.1], p = .004). CONCLUSIONS: Type 1A has a high survival rate in studies reporting strict patient and site selection criteria. Further research is required to assess esthetic and functional success with Type 1A treatments.

Group 5 ITI Consensus Report: Implant placement and loading protocols.

OBJECTIVES: Working Group 5 was convened to discuss and find consensus on the topics of implant placement and loading protocols associated with single missing teeth in the anterior maxilla (aesthetic zone). Consensus statements, clinical recommendations, patient perspectives and future research suggestions were developed and presented to the plenary for discussion and approval. MATERIALS AND METHODS: Two systematic reviews were developed and submitted prior to the conference. The group considered in detail the systematic reviews and developed statements, clinical recommendations, patient perspectives and future research suggestions based on the findings of the reviews and experience of group members. Definitive versions were developed after presentation to and discussion by the plenary. RESULTS: Five consensus statements were developed and approved from each systematic review. Twelve clinical recommendations were developed by the group based on both reviews and experience. Three patient perspectives were developed, and five suggestions made for future research. CONCLUSIONS: Based on the findings of the systematic reviews and experience of group members, the Type 1A protocol (immediate placement and immediate loading), when utilized in the anterior maxilla under favorable conditions, is considered predictable and is associated with high survival rates. The procedure is considered clinically viable and is associated with aesthetic outcomes, although surgical, technical, and biological complications can occur.

A spectrum of verticality across genes.

Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the factors that govern LGT frequency across genes. Estimating LGT frequency from tree comparisons is problematic when thousands of genomes are compared, because LGT becomes difficult to distinguish from phylogenetic artefacts. Here we report quantitative estimates for verticality across all genes and genomes, leveraging a well-known property of phylogenetic inference: phylogeny works best at the tips of trees. From terminal (tip) phylum level relationships, we calculate the verticality for 19,050,992 genes from 101,422 clusters in 5,655 prokaryotic genomes and rank them by their verticality. Among functional classes, translation, followed by nucleotide and cofactor biosynthesis, and DNA replication and repair are the most vertical. The most vertically evolving lineages are those rich in ecological specialists such as Acidithiobacilli, Chlamydiae, Chlorobi and Methanococcales. Lineages most affected by LGT are the α-, ß-, γ-, and δ- classes of Proteobacteria and the Firmicutes. The 2,587 eukaryotic clusters in our sample having prokaryotic homologues fail to reject eukaryotic monophyly using the likelihood ratio test. The low verticality of α-proteobacterial and cyanobacterial genomes requires only three partners-an archaeal host, a mitochondrial symbiont, and a plastid ancestor-each with mosaic chromosomes, to directly account for the prokaryotic origin of eukaryotic genes. In terms of phylogeny, the 100 most vertically evolving prokaryotic genes are neither representative nor predictive for the remaining 97% of an average genome. In search of factors that govern LGT frequency, we find a simple but natural principle: Verticality correlates strongly with gene distribution density, LGT being least likely for intruding genes that must replace a preexisting homologue in recipient chromosomes. LGT is most likely for novel genetic material, intruding genes that encounter no competing copy.