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In the continuity of a previous jet-cooled rovibrational study of trans and cis conformers of 2-furfural in the mid-infrared region (700–1750 cm−1) [Chawananon et al., Molecules 28 (10), 4165 (2023)], the present work investigates the far-infrared spectroscopy of 2-furfural using a long path absorption cell coupled to a high-resolution Fourier transform spectrometer and synchrotron radiation at the AILES beamline of the SOLEIL synchrotron. Guided by anharmonic calculations, vibrational energy levels and excited-state rotational constants are sufficiently predictive for a complete assignment of all fundamental and combination bands up to 700 cm−1, as well as the rovibrational analysis of 4 (1) low-frequency modes of trans-(cis-)2-furfural. A global rovibrational simulation, including far-infrared rovibrational lines and microwave and millimeter-wave rotational lines assigned in a previous study [Motiyenko et al., J. Mol. Spectrosc., 244, 9 (2007)] provides a reliable set of ground- and excited-state rotational parameters involving ring torsion, bending, and ring puckering modes of 2-furfural. In a second step, a rovibrational analysis of several hot band sequences, mainly involving the lowest frequency ring CHO torsion mode, is carried out. Reliable values of some anharmonic coefficients are obtained experimentally and could serve as a benchmark for validating advanced anharmonic calculations related to these large amplitude motions of flexible molecules. [ABSTRACT FROM AUTHOR]

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [i.e., untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed alternative proteins (altProts). This suggests that previously identified protein–protein interaction (PPI) networks are partially incomplete because altProts are not present in conventional protein databases. Here, we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset, thereby revealing the presence of 261 altProts in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 117 altProts encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental genes. Finally, we experimentally validate several interactions involving altProts. These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.

Abstract Background Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed. Results We found a downstream alternative ATG initiation codon in the + 3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology. Conclusions Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.

Abstract Background Recent technological advances have revealed thousands of functional open reading frames (ORF) that have eluded reference genome annotations. These overlooked ORFs are found throughout the genome, in any reading frame of transcripts, mature or non-coding, and can overlap annotated ORFs in a different reading frame. The exploration of these novel ORFs in genomic datasets and of their role in genetic traits is hindered by a lack of software. Results Here, we present OpenVar, a genomic variant annotator that mends that gap and fosters meaningful discoveries. To illustrate the potential of OpenVar, we analysed all variants within SynMicDB, a database of cancer-associated synonymous mutations. By including non-canonical ORFs in the analysis, OpenVar yields a 33.6-fold, 13.8-fold and 8.3-fold increase in high impact variants over Annovar, SnpEff and VEP respectively. We highlighted an overlapping non-canonical ORF in the HEY2 gene where variants significantly clustered. Conclusions OpenVar integrates non-canonical ORFs in the analysis of genomic variants, unveiling new research avenues to better understand the genotype–phenotype relationships.

Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.

The physical mechanisms associated with heat waves (HWs) are well known in the midlatitudes but still under-documented in the Sahel. Specifically, the role of anthropogenic and natural changes in tropospheric aerosols regarding HWs remains an issue to address. Our study focuses on the characterisation of the dusty HWs in the Sahel, which generally occur from March to June. The goal is to reinforce or invalidate the assumption proposed in previous studies recently carried out in southern Europe and according to which mineral dust may locally change irradiance at the surface, thus atmospheric temperatures at 2 m, intensifying the HW. The work is carried out in three steps: (i) detect and describe the HW over the 2003–2014 period based on maximum daily 2-m temperatures (Tmax) from ERA-Interim reanalyses; (ii) characterise the dust optical properties during the HW using the Deep Blue aerosols products from MODIS (Moderate Resolution Imaging Spectroradiometre): the Aerosol Optical Depth at 550 nm (AOD550), the Angstrom Exponent (AE440−870) and the Single Scattering Albedo at 412 nm (SSA412) as a proxy of quantity over atmospheric column, size and absorption of aerosols, respectively; (iii) relate HW intensity to the aerosol conditions during the HW. Over the 12-year study period, 14 HWs are detected when Tmax exceeds the 90th percentile (P90). The HWs are dusty with AOD550 ranging between 0.46 and 1.17 and all the dust types are absorbent with a SSA412 value of 0.93 (round to hundredths). The HW classification according to aerosol conditions gave three HWs: Type 1 corresponds to Pure Dust Situation (PDS with AE440−870 = 0.1), Type 2 and Type 3 are associated with Mixed Situation (MS) with dominance of Coarse Particles (CP with AE440−870 = 0.35) and Fine Particles (FP with AE440−870 = 0.65), respectively. The main result obtained is that the intensity of the dusty HW, computed as the difference between daily Tmax and its P90 (Tmax−P90)), is higher for Type 1 HW (+1.1 °C) in the case of the most absorbent aerosol situation (SSA412 = 0.931). A non-significant difference between Type 2 and Type 3 especially for temperature (+0.5 °C and +0.4 °C, respectively) and SSA (0.938 and 0.935, respectively) is observed and, during these mixing situations, the HWs are less intense than those during the PDS. Finally, the analysis of two huge Type 1 HWs in 2007 and 2010 shows that dust mass concentrations at the surface were particularly high, up to 214 μg/m3 on average. These findings enable us to assess that highly absorbent and concentrated pure dust situations observed in spring in the Sahel may have a potential warming effect at the surface.

The blood–brain barrier (BBB) is a major obstacle to the development of effective therapeutics for central nervous system (CNS) disorders, including Alzheimer’s disease (AD). This has been particularly true in the case of monoclonal antibody (mAbs) therapeutic candidates, due to their large size. To tackle this issue, we developed new nanoformulations, comprising bio-based Triozan polymers along with kinin B1 and B2 receptor (B1R and B2R) peptide agonist analogues, as potent BBB-permeabilizers to enhance brain delivery of a new anti-C1q mAb for AD (ANX005). The prepared B1R/B2R-TRIOZAN™ nanoparticles (NPs) displayed aqueous solubility, B1R/B2R binding capacity and uniform sizes (~130–165 nm). The relative biodistribution profiles of the mAb loaded into these NPs versus the naked mAb were assessed in vivo through two routes of administrations (intravenous (IV), intranasal (IN)) in the Tg-SwDI mouse model of AD. At 24 h post-administration, brain levels of the encapsulated mAb were significantly increased (up to 12-fold (IV) and 5-fold (IN), respectively) compared with free mAb in AD brain affected regions, entorhinal cortex and hippocampus of aged mice. Liver uptakes remained relatively low with similar values for the nanoformulations and free mAb. Our findings demonstrate the potential of B1R/B2R-TRIOZAN™ NPs for the targeted delivery of new CNS drugs, which could maximize their therapeutic effectiveness.

Translation involves the biosynthesis of a protein sequence following the decoding of the genetic information embedded in a messenger RNA (mRNA). Typically, the eukaryotic mRNA was considered to be inherently monocistronic, but this paradigm is not in agreement with the translational landscape of cells, tissues, and organs. Recent ribosome sequencing (Ribo-seq) and proteomics studies show that, in addition to currently annotated reference proteins (RefProt), other proteins termed alternative proteins (AltProts), and microproteins are encoded in regions of mRNAs thought to be untranslated or in transcripts annotated as non-coding. This experimental evidence expands the repertoire of functional proteins within a cell and potentially provides important information on biological processes. This review explores the hitherto overlooked alternative proteome in neurobiology and considers the role of AltProts in pathological and healthy neuromolecular processes.

The ortho-isomer 2-furfural (2-FF), which is a primary atmospheric pollutant produced from biomass combustion, is also involved in oxidation processes leading to the formation of secondary organic aerosols. Its contribution to radiative forcing remains poorly understood. Thus, monitoring 2-FF directly in the atmosphere or in atmospheric simulation chambers to characterize its reactivity is merited. The present study reports an extensive jet-cooled rovibrational study of trans and cis conformers of 2-FF in the mid-IR region using two complementary setups: a continuous supersonic jet coupled to a high-resolution Fourier transform spectrometer on the IR beamline of the SOLEIL synchrotron (JET-AILES), and a pulsed jet coupled to a mid-IR tunable quantum cascade laser spectrometer (SPIRALES). Firstly, jet-cooled spectra recorded at rotational temperatures ranging between 20 and 50 K were exploited to derive reliable excited-state molecular parameters of trans- and cis-2-FF vibrational bands in the fingerprint region. The parameters were obtained from global fits of 11,376 and 3355 lines distributed over eight and three vibrational states (including the ground state), respectively, with a root mean square of 12 MHz. In a second step, the middle resolution spectrum of 2-FF recorded at 298.15 K and available in the HITRAN database was reconstructed by extrapolating the data derived from our low-temperature high-resolution analyses to determine the cross sections of each vibrational band of both 2-FF conformers in the 700–1800 cm−1 region. Finally, we clearly demonstrated that the contribution of hot bands observed in the room temperature 2-FF spectrum, estimated between 40 and 63% of the fundamental band, must be imperatively introduced in our simulation to correctly reproduce the HITRAN vibrational cross sections of 2-FF with a deviation smaller than 10%.

During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.

We present the measurement and analysis of the 2OH stretching band of methanol between 7165 cm−1 and 7230 cm−1 cooled down to 26 ± 12 K in a buffer gas cooling experiment. Measurements were performed with a cavity ring-down spectrometer having a detection limit αmin = 2 × 10−10 cm−1. A total of 350 rovibrational transitions were assigned and 62 rovibrational transitions were tentatively assigned. This assignment was performed using the pattern recognition method developed by Rakvoský et al. [Phys. Chem. Chem. Phys., 2021, 23, 20193–20200]. In this work, we extended their method by using information on the relative intensities of the transitions to add one criterion to the validation of the assignments, allowing us to firmly assign 188 additional rovibrational transitions and to tentatively assign 14 more compared to the ir work. [ABSTRACT FROM AUTHOR]

Abstract Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations.

Ubiquitin pseudogenes are present in many organisms but whether they encode functional proteins has remained unclear. Here, the authors show that human UBB pseudogene 4 produces ubiquitin variants with amino acid compositions and cellular functions that are distinct from canonical ubiquitin.

Methylfurans are methylated aromatic heterocyclic volatile organic compounds and primary or secondary pollutants in the atmosphere due to their capability to form secondary organic aerosols in presence of atmospheric oxidants. There is therefore a significant interest to monitor these molecules in the gas phase. High resolution spectroscopic studies of methylated furan compounds are generally limited to pure rotational spectroscopy in the vibrational ground state. This lack of results might be explained by the difficulties arisen from the internal rotation of the methyl group inducing non-trivial patterns in the rotational spectra. In this study, we discuss the benefits to assign the mm-wave rotational-torsional spectra of methylfuran with the global approach of the BELGI-Cs code compared to local approaches such as XIAM and ERHAM. The global approach reproduces the observed rotational lines of 2-methylfuran and 3-methylfuran in the mm-wave region at the experimental accuracy for the ground vt=0 and the first torsional vt=1 states with a unique set of molecular parameters. In addition, the V3 and V6 parameters describing the internal rotation potential barrier may be determined with a high degree of accuracy with the global approach. Finally, a discussion with other heterocyclic compounds enables the study of the influence of the electronic environment on the hindered rotation of the methyl group.

Physiological and biochemical networks are highly complex, involving thousands of nodes as well as a hierarchical structure. True network structure is also rarely known. This presents major challenges for applying classical network theory to these networks. However, complex systems generally share the property of having a diffuse or distributed signal. Accordingly, we should predict that system state can be robustly estimated with sparse sampling, and with limited knowledge of true network structure. In this review, we summarize recent findings from several methodologies to estimate system state via a limited sample of biomarkers, notably Mahalanobis distance, principal components analysis, and cluster analysis. While statistically simple, these methods allow novel characterizations of system state when applied judiciously. Broadly, system state can often be estimated even from random samples of biomarkers. Furthermore, appropriate methods can detect emergent underlying physiological structure from this sparse data. We propose that approaches such as these are a powerful tool to understand physiology, and could lead to a new understanding and mapping of the functional implications of biological variation.

Introduction Vasodilatory hypotension is common among intensive care unit (ICU) patients; vasopressors are considered standard of care. However, optimal mean arterial pressure (MAP) targets for vasopressor titration are unknown. The objective of the Optimal VAsopressor TitraTION in patients 65 years and older (OVATION-65) trial is to ascertain the effect of permissive hypotension (vasopressor titration to achieve MAP 60–65 mm Hg) versus usual care on biomarkers of organ injury in hypotensive patients aged ≥65 years.Methods and analysis OVATION-65 is an allocation-concealed randomised trial in 7 Canadian hospitals. Eligible patients are ≥65 years of age, in an ICU with vasodilatory hypotension, receiving vasopressors for ≤12 hours to maintain MAP ≥65 mm Hg during or after adequate fluid resuscitation, and expected to receive vasopressors for ≥6 additional hours. Patients are excluded for any of the following: active treatment for spinal cord or acute brain injury; vasopressors given solely for bleeding, ventricular failure or postcardiopulmonary bypass vasoplegia; withdrawal of life-sustaining treatments expected within 48 hours; death perceived as imminent; previous enrolment in OVATION-65; organ transplant within the last year; receiving extracorporeal life support or lack of physician equipoise. Patients are randomised to permissive hypotension versus usual care for up to 28 days. The primary outcome is high-sensitivity troponin T, a biomarker of cardiac injury, on day 3. Secondary outcomes include biomarkers of injury to other organs (brain, liver, intestine, skeletal muscle); lactate (a biomarker of global tissue dysoxia); resource utilisation; adverse events; mortality (90 days and 6 months) and cognitive function (6 months). Assessors of biomarkers, mortality and cognitive function are blinded to allocation.Ethics and dissemination This protocol has been approved at all sites. Consent is obtained from the eligible patient, the substitute decision-maker if the patient is incapable, or in a deferred fashion where permitted. End-of-grant dissemination plans include presentations, publications and social media platforms and discussion forums.Trial registration number NCT03431181.

The levels of deoxynivalenol (DON)—a mycotoxin produced by Fusarium graminearum—in maize for food and feed are subject to European Union regulations. Obtaining a compliant harvest requires the identification of agronomic and climatic risk factors related to higher fungal contamination and DON production. A national, multiyear database for maize was created, based on field survey data collected from 2004 to 2020. This database contains information about agricultural practices, climatic sequences and DON content at harvest for a total of 2032 maize fields localized in the French maize-growing regions. A linear mixed-model approach highlighted the presence of borers, late harvest and inadequate crop residue management, normal-to-cold temperatures in March, humidity in August and the absence of a hot end of the maize development cycle with a dry August as creating conditions favoring maize contamination with DON. The various possible associations between these risky climatic conditions and agricultural practices were compared, grouped and ranked as related to very low to high DON concentrations. Some combinations may even exceed the regulatory threshold. The national prevention tool, created for producers and agricultural cooperatives, is informative and easy-to-use to control the sanitary quality of their harvest.