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PubMed2026

Metagenome-resolved evidence that soluble factors in granular activated carbon-amended reactor effluent reprogram propionate metabolism and methanogenic pathways.

Granular activated carbon (GAC) enhances anaerobic digestion performance, yet the mechanisms underlying reactor-scale improvements remain incompletely understood, particularly how GAC affects biomass not attached to its surface. Here, sludge from a non-GAC up-flow anaerobic sludge blanket reactor was incubated with 0.45-μm-filtered effluents from non-GAC and GAC-amended reactors under repeated propionate loading, followed by genome-resolved metagenomics. GAC-reactor effluent increased methane yield from 64 ± 3% to 76 ± 3% (p < 0.01) in the absence of GAC particles. A non-redundant catalog of 170 quality-filtered metagenome-assembled genomes (MAGs) was recovered, enabling pathway- and gene-set quantification. Genomic potential for both major propionate-oxidation routes increased in the GAC-effluent group relative to the non-GAC group, with a larger increase for the methylmalonyl-CoA (MMC) route than for the dismutation route (1.289- versus 1.221-fold). Accordingly, the MMC-to-dismutation preference ratio was 5.60% higher in the GAC-effluent group, alongside a broader carrier base. Cobamide potential shifted toward remodeling and cobamide-dependent use rather than increased de novo corrin-ring synthesis. Candidate electron-transfer architectures were also rebalanced: PilA-associated carriers became less prominent, whereas maturation-supported multiheme cytochrome carriers increased from 22.96% to 34.90% of community abundance, although H2/formate-module carriers remained prevalent. Quorum-sensing systems underwent pathway- and carrier-specific redistribution, while all eight curated extracellular-polysaccharide modules showed higher mean gene abundance in the GAC-effluent composite. These findings show that a filter-passing effluent fraction can extend GAC-associated effects beyond direct particle contact and link enhanced methanogenesis to a broader, redistributed network of metabolic, redox, and coordination capacities. This expands the mechanistic framework of conductive-material-assisted anaerobic digestion and provides a basis for harnessing GAC-derived functions throughout the reactor.

Extracellular polymeric substances (EPS)↗

PubMed2005

A survey of potential huperzine A natural resources in China: the Huperziaceae.

The Huperziaceae is comprised of two genera, Huperzia and Phlegmariurus. Because of the content of Lycopodium alkaloids like huperzine A, which are used to treat a number of human ailments, plants of the Huperziaceae are experiencing a rapid decline in China, mostly due to over-harvesting. Because of this trend, we engaged from 1995 to 2001 in an investigation of the natural resources of the Huperziaceae in China. The main objectives of this study were: to catalog Huperziaceae plant resources including the occurrence, general distribution, and abundance of the various Huperziaceae species in China; and to determine traditional use and pharmaceutical values of each species. Twenty-nine species, 2 varieties, and 2 forma of Huperzia and 19 species of Phlegmariurus were identified through field investigation, collection, visits with local traditional doctors, and review of specimens in herbaria and of the literature. Ethnobotanical studies of these plants revealed that 33 of these species are used by the local communities for medicinal purposes. One species, Huperzia serrata, is one of the most popular. As a result, it is observing the greatest decline, mandating a change in collection practice and general attitude towards these plants. Introduction of conservation plans and training of the local communities regarding appropriate collection practices of these plants and their marketing in China are required to reverse the trend of decline among these species. In addition, development of cultivation or other propagation practices, such as in vitro propagation, would have the added benefits of socio-economic uplift of the local communities and sustainability of this important source of huperzine A.

Alkaloids↗

PubMed2026

The bioinformatics approach to identifying pathogenic variants for colorectal cancer (CRC).

Colorectal cancer (CRC) is the third most prevalent cancer globally, accounting for 9.6% of newly diagnosed cases and 9.3% of cancer-related deaths. It develops from the uncontrolled proliferation of glandular cells in the colon and rectum and is categorized into three primary types: sporadic, hereditary, and colitis-associated. While genetic susceptibility is a key factor in CRC pathogenesis, identifying high-impact pathogenic variants remains a significant challenge. This study integrates bioinformatics and population genetics approaches to identify CRC-associated single-nucleotide polymorphisms (SNPs) with potential clinical significance. CRC-associated SNPs were extracted from the Genome-Wide Association Studies (GWAS) Catalog, functionally annotated via HaploReg, and validated via Ensembl. In addition, expression quantitative trait locus (eQTL) data from the GTEx database were used to assess the effects of these variants on gene expression across human tissues. Our analysis identified three high-priority SNPs (rs9379084, rs3184504, and rs11557154) associated with the RREB1, ATXN2, SH2B3, and DCAF12 genes, which exhibited marked allele frequency differences among populations. These findings suggest potential biomarkers for CRC risk assessment and highlight the importance of genetic screening across diverse populations.

Bioinformatics↗

PubMed2026

Current landscape of Cys-OxiPTMs in plants: from hormone signaling to phenotypic control and their potential in sustainable agriculture.

The integration of environmental and developmental cues into coherent physiological responses is fundamental to plant survival. Reactive oxygen, nitrogen, and sulfur species (ROS/RNS/RSS) are now recognized as essential signaling molecules, not merely cytotoxic byproducts. Their specificity is largely achieved through reversible, site-specific cysteine oxidative post-translational modifications (Cys-OxiPTMs), which constitute a dynamic and sophisticated "redox code". This review provides a systematic synthesis of the current landscape of Cys-OxiPTMs in plants, bridging chemistry, hormone biology, agronomy, detection, and engineering. The chemical and enzymatic basis of major Cys-OxiPTMs is detailed, along with a discussion of how their spatiotemporal interplay orchestrates signaling specificity. A critical examination is then presented on how these modifications decode and integrate plant hormone signaling networks to regulate key agronomic traits. Cutting-edge proteomic technologies that have revolutionized the identification of redox-sensitive cysteines are also evaluated. Finally, forward-looking strategies to "write" the redox code are explored. By moving the field from descriptive cataloging to predictive "redox breeding", this review establishes a foundational framework for manipulating Cys-OxiPTMs to develop climate-resilient, high-yielding crops for sustainable agriculture.

Agronomic traits↗

PubMed2005

Multiple functions of a feed-forward-loop gene circuit.

The feed-forward-loop (FFL), a network motif in genetic regulatory networks, involves two transcription factors (TFs): one regulates the expression of the second, and both TFs regulate the expression of an effector gene. Analysis of FFL design principles has been initiated, but the functional significance of the FFL is still unclear. In theoretical studies so far, the TFs are assumed to interact with different signals, which is common. However, we have found examples of FFLs in Escherichia coli in which both TFs interact with the same signal. These examples belong to the type 2 incoherent class of FFLs, in which each TF acts exclusively as a repressor of transcription. Here, we analyze mathematical models of this class of circuits, examining a comprehensive array of subclasses that differ in the way a signal modulates the activities of the TFs. Through parameter variation, we characterize statistically how input/output (I/O) behavior and temporal responsiveness are predicted to depend on the wiring of signal interactions in a circuit. We find that circuits can exhibit any of 13 qualitatively distinct steady-state I/O patterns, including inducible and repressible patterns. Some subclasses exhibit as many as six patterns. Transient pulses are also possible, and the response of a circuit to a signal may be either faster or slower than that of a gene circuit in which there is only one TF. Our results provide a catalog of functions for a class of FFL circuits, whose subclasses have different breadths of possible behaviors and different typical behaviors.

Escherichia coli↗

PubMedDate not supplied

Update on nonpharmacologic approaches to relieve labor pain and prevent suffering.

The control of labor pain and prevention of suffering are major concerns of clinicians and their clients. Nonpharmacologic approaches toward these goals are consistent with midwifery management and the choices of many women. We undertook a literature search of scientific articles cataloged in CINAHL, PUBMED, the Cochrane Library, and AMED databases relating to the effectiveness of 13 non-pharmacologic methods used to relieve pain and reduce suffering in labor. Suffering, which is different from pain, is not an outcome that is usually measured after childbirth. We assumed that suffering is unlikely if indicators of satisfaction were positive after childbirth. Adequate evidence of benefit in reducing pain exists for continuous labor support, baths, intradermal water blocks, and maternal movement and positioning. Acupuncture, massage, transcutaneous electrical nerve stimulation, and hypnosis are promising, but they require further study. The effectiveness of childbirth education, relaxation and breathing, heat and cold, acupressure, hypnosis, aromatherapy, music, and audioanalgesia are either inadequately studied or findings are too variable to draw conclusions on effectiveness. All the methods studied had evidence of widespread satisfaction among a majority of users.

Acupuncture Analgesia↗

PubMed2005

Health-related disparities: influence of environmental factors.

Racial disparities in health cannot be explained solely on the basis of poverty, access to health care, behavior, or environmental factors. Their complex etiology is dependent on interactions between all these factors plus genetics. Scientists have been slow to consider genetics as a risk factor because genetic polymorphisms tend to be more variable within a race than between races. Now that studies are demonstrating the existence of racial differences in allelic frequencies for multiple genes affecting a single biologic mechanism, the present argument for a significant genetic role in contributing to health disparities is gaining support. Individuals vary, often significantly, in their response to environmental agents. This variability provides a high "background noise" when scientists examine human populations to identify environmental links to disease. This variability often masks important environmental contributors to disease risk and is a major impediment to efforts to investigate the causes of diseases.Fortunately, investments in the various genome projects have led to the development of tools and databases that can be used to help identify the genetic variations in environmental response genes that can lead to such wide differences in disease susceptibility. NIEHS developed the environ-mental genome project to catalog these genetic variants (polymorphisms)and to identify the ones that play a major role in human susceptibility to environmental agents. This information is being used in epidemiologic studies to pinpoint environmental contributors to disease better. The research summarized in this article is critically important for tying genetics and the environment to health disparities, and for the development of a rational approach to gauge environmental threats. Common variants in genes play pivotal roles in determining if or when illness or death result from exposure to drugs or environmental xenobiotics. Most common variants exist in all human populations, but their frequency can vary substantially,rendering individuals or groups more or less susceptible to particular environmental exposures. Such findings are consistent with the highly publicized analogy, "genetics loads the gun, but the environment pulls the trigger." That is, one can inherit the genetic predisposition to develop a disease but will do so only if or when exposed to the environmental trigger. Poor people have approximately the same genetic makeup as everyone else,but they have the unfortunate experience of living and working in environments containing multiple and high levels of carcinogens or other toxicants capable of interacting with susceptibility genes to cause disease.Furthermore, certain disadvantaged ethnic groups may have a higher incidence of certain susceptible genes that render them more vulnerable to adverse effects of the environments they inhabit. For both of these reasons,much of the nation's disease burden could likely be reduced through better environmental protection practices, especially in low-income and minority communities. Of the many implications of polymorphisms and frequency variations for public health and the practice of medicine, however, none is more urgent than the choice of drugs in therapy. Using such knowledge,randomized trials have identified race-specific drug response differences between blacks and whites [42].To date, most knowledge of the health effects of environmental factors is derived from studies of single agents. The reality, though, is that environmental contributions to health disparities are mostly from multiple agents. These simultaneous exposures to multiple risk factors, which may accumulate or interact synergistically, remain to be fully explained and defined.Finally, health disparity is a significant public health problem that cannot be solved using "business as usual" approaches for funding and priority setting. The current emphasis on basic and clinical research at the exclusion of public health and the social sciences does not provide the interdisciplinary research teams necessary to address such a complex problem as health disparities. Although the poor will always be with us, their health could be greatly improved if social, environmental, and genetic scientists could find ways to collaborate and develop more insightful and relevant ways to address the health of disadvantaged communities.

Delivery of Health Care↗

PubMed2004

Patterning and tissue movements in a novel explant preparation of the marginal zone of Xenopus laevis.

Development of the Xenopus embryo has provided an adaptable framework for the rapid evaluation of molecular factors that guide patterning and morphogenesis. We present and characterize a novel explant preparation that is useful for such studies. This preparation consists of 180 degrees of the marginal zone of the early Xenopus gastrula cultured on a fibronectin-coated substrate. In addition to a thorough description of its preparation, we analyze gene expression patterns at three stages of development. The stereotypic morphogenesis of this explant can be understood in the context of the intact embryo through a catalog of gene expression patterns providing definitive identities for epidermis, anterior and posterior neural, notochord, somitic mesoderm, and mesendoderm.

Animals↗

PubMed2005

Reading, hearing, and the planum temporale.

Many neuroimaging studies of single-word reading have been carried out over the last 15 years, and a consensus as to the brain regions relevant to this task has emerged. Surprisingly, the planum temporale (PT) does not appear among the catalog of consistently active regions in these investigations. Recently, however, several studies have offered evidence suggesting that the left posteromedial PT plays a role in both speech production and speech perception. It is not clear, then, why so many neuroimaging studies of single-word reading--a task requiring speech production--have tended not to find evidence of PT involvement. In the present work, we employed a high-powered rapid event-related fMRI paradigm involving both single pseudoword reading and single pseudoword listening to assess activity related to reading and speech perception in the PT as a function of the degree of spatial smoothing applied to the functional images. We show that the speech area of the PT [Sylvian-parietal-temporal (Spt)] is best identified when only a moderate (5 mm) amount of spatial smoothing is applied to the data before statistical analysis. Moreover, increasing the smoothing window to 10 mm obliterates activation in the PT, suggesting that failure to find PT activation in past studies may relate to this factor.

Adult↗

PubMed2026

Mapping cell-type- and age-dependent neuronal vulnerability through genome-wide in vivo CRISPRi screens in the mouse brain.

Current brain atlases are largely descriptive, cataloging correlative molecular snapshots such as gene expression signatures yet offering limited functional insight. Here, we develop a scalable, cell-type-resolved in vivo CRISPR interference (CRISPRi) platform enabling systematic gene function profiling in the mouse brain. Through genome-wide screens across four neuronal populations at three time points spanning youth to aging, we identify neuronal essential genes missed in vitro and define a consensus set of 269 neuronal core essential genes. The data reveal cell-type-specific genetic vulnerabilities, including divergent dependencies validated for exosome component 9 (Exosc9) and osteopetrosis-associated transmembrane protein 1 (Ostm1) between excitatory and inhibitory neurons. We uncover aging-specific dependencies enriched in mitochondrial and translational pathways, aligning with transcriptional changes in the aging human brain. Finally, we establish the CRISPRinvivo data portal as a community resource for in vivo screening. Altogether, this work provides a broadly applicable platform for in vivo functional genomics and a framework for building comprehensive gene-function brain atlases.

brain aging↗

PubMed2005

Nitrosative stress results in irreversible inhibition of purified mitochondrial complexes I and III without modification of cofactors.

The effects of both nitric oxide (NO) and peroxynitrite on complexes I (NADH dehydrogenase) and III (cytochrome c reductase) isolated from bovine heart have been examined. EPR signals ("g=2.01") previously detected in association with loss of complex I and III activities in cultured cells and isolated mitochondria subjected to nitrosative stress are shown not to arise from these particular enzymes. Neither NO nor peroxynitrite (ONO(2)(-)) reacts to any appreciable extent with the oxidized forms of flavin mononucleotide, iron-sulfur clusters, or heme moieties found in complexes I and III. However, ONO(2)(-) is readily able to abstract electrons from the reduced forms of both complexes I and III, without any apparent modification of the enzyme cofactors. While no attempt was made in the present study to catalog all the possible modifications, it is clear that ONO(2)(-) can react with the protein moieties of the enzymes. For example, when added in excess, ONO(2)(-) derivatizes a select few tyrosine residues in both complexes I and III forming 3-nitrotyrosine as detected by immunoblots. In the case of complex I, we find a minimum of 3 out of the 46 subunits present were modified (49, approximately 18, and approximately 15kDa); whereas in complex III, 4 out of the 13 subunits stained for 3-nitrotyrosine (46, 27, 7, and 6kDa). Significant irreversible inhibition of activity required the addition of >10(2)-fold excesses of ONO(2)(-) to the enzymes. At 10(3)-fold excess of added ONO(2)(-), the activity of complex I was only diminished by approximately 18%, while a 60% loss of activity was observed for complex III.

Animals↗

PubMed2006

Fundus autofluorescence in patients with pseudoxanthoma elasticum.

PURPOSE: To evaluate the autofluorescence findings of patients with pseudoxanthoma elasticum, a disease resulting from a defect in a reputed transport protein encoded by the gene adenosine triphosphate-binding cassette subtype C number 6. DESIGN: Observational case series. METHODS: Color, red-free monochromatic, and autofluorescence photography and fluorescein angiography of patients with pseudoxanthoma elasticum seen in a referral practice were evaluated. MAIN OUTCOME MEASURES: Cataloging of the abnormalities as detected by autofluorescence photography. RESULTS: The 8 subjects ranged in age from 26 to 60 years (mean, 55+/-12), and their best-corrected visual acuity ranged from 20/20 to 5/400 (mean, 20/50). Of the 16 eyes of the 8 patients, all had abnormalities typical of pseudoxanthoma elasticum, including angioid streaks in 14, peau d'orange in 4, and choroidal neovascularization in 11. Angioid streaks appeared as hypoautofluorescent fissures, sometimes showing expansion of the hypoautofluorescence suggestive of retinal pigment epithelium (RPE) absence or atrophy. Peau d'orange had a stippled appearance of autofluorescence, and drusen of the optic nerve appeared as hyperautofluorescent bodies. In addition to the expansion of RPE atrophy around angioid streaks, 3 additional configurations of RPE atrophy were recognized as RPE rips in 6 eyes, multilobular areas of atrophy in 9 eyes, and broad areas of poorly demarcated atrophy in 5 eyes. Some eyes had more than one manifestation of RPE atrophy, but the latter 3 types of atrophy occurred in eyes with, but not necessary contiguous to, concurrent choroidal neovascularization. CONCLUSIONS: Autofluorescence photography demonstrated that patients with pseudoxanthoma elasticum have more widespread areas of RPE disturbance, particularly atrophy, than what is detectable by other means of ocular imaging, which suggests that the RPE disturbance may play a role in the pathogenesis of visual loss in patients with pseudoxanthoma elasticum.

Adult↗

PubMed2004

The plot thickens: New perspectives of primary cell wall modification.

Recent studies have further confirmed the ubiquity of cell wall restructuring during plant growth and development, and have emphasized the fact that our understanding of the breadth of molecular processes that mediate wall modification is still rudimentary. In the past few years, both enzymatic and non-enzymatic agents that apparently contribute to wall disassembly have been identified, and it is likely that additional mechanisms will continue to be revealed. These discoveries are being propelled by the development of new biochemical and biophysical assays, by database mining in the wake of the explosion of plant sequence information from genome sequencing and expressed sequence tags, and by a variety of strategies used to catalog the cell wall proteome. The daunting question of how these mechanistically diverse and complex processes are coordinated remains unresolved.

Arabidopsis↗

PubMed2005

Bioinformatic analysis of neuropeptide and receptor expression profiles during midgut metamorphosis in Drosophila melanogaster.

Neuropeptides are important messenger molecules in invertebrates, serving as neuromodulators in the nervous system and as regulatory hormones released into the circulation. Understanding the function of neuropeptides will require the integration of genetic, biochemical, physiological and behavioral information. The advent of DNA microarrays and bioinformatic databases provides a wealth of data describing the expression profiles of thousands of genes during biological processes. One such array catalogs the developmental patterns of gene expression during the metamorphic transformation of the Drosophila midgut. We have mined the data from this experiment to explore changes of expression in genes coding for known neuropeptides, peptide hormones, and their receptors during the metamorphosis of the midgut. We found small but significant changes in the expression of the peptides diuretic hormone, FGLa-type allatostatins, myoinhibiting peptide, ecdysis-triggering hormone, drosokinin and the burs subunit of bursicon, as well as the receptors DAR-2, NPFR1, ALCR-2, Lkr and DH-R. Just as advances have been made in understanding the molecular basis of invertebrate neuropeptide action by analysis of genome projects, data mining of gene expression databases can help to integrate molecular, biochemical and physiological knowledge of biological processes.

Animals↗

PubMed2005

Digging deeper into the plant cell wall proteome.

The proteome of the plant cell wall/apoplast is less well characterized than those of other subcellular compartments. This largely reflects the many technical challenges involved in extracting and identifying extracellular proteins, many of which resist isolation and identification, and in capturing a population that is both comprehensive and relatively uncontaminated with intracellular proteins. However, a range of disruptive techniques, involving tissue homogenization and subsequent sequential extraction and non-disruptive approaches has been developed. These approaches have been complemented more recently by other genome-scale screens, such as secretion traps that reveal the genes encoding proteins with N-terminal signal peptides that are targeted to the secretory pathway, many of which are subsequently localized in the wall. While the size and complexity of the wall proteome is still unresolved, the combination of experimental tools and computational prediction is rapidly expanding the catalog of known wall-localized proteins, suggesting the unexpected extracellular localization of other polypeptides and providing the basis for further exploration of plant wall structure and function.

Cell Wall↗

PubMed2004

A primer on expanded newborn screening by tandem mass spectrometry.

Newborn screening (NBS) for a wide variety of inborn errors of metabolism using the powerful tool of tandem mass spectrometry (MS/MS) is becoming widespread. This article provides the basic information that primary care clinicians need to help make rational decisions about urgent evaluation and appropriate follow-up of patients with abnormal expanded NBS tests. Also outlined are ways that the screening tests can be inaccurate. A normal MS/MS NBS result does not rule out the possibility of an inborn error of metabolism in an infant with acute illness, developmental abnormalities,or other clinically suggestive conditions. Primary care practitioners should identify the metabolic specialists in their area and develop a relationship with them to ensure clear communication when abnormal results arrive. Included in this article is a catalog of "thumbnail sketches" for reference by physicians when they receive an abnormal MS/MS NBS result.

Humans↗

PubMed2005

Targeting malaria parasite proteins to the erythrocyte.

The intraerythrocytic stages of the protozoan parasite Plasmodium falciparum reside within a parasitophorous vacuole (PV) and set up unique "extraparasite, intraerythrocyte" protein-trafficking pathways that target parasite-encoded proteins to the erythrocyte cytoplasm and cell surface. Two recent articles report the identification of trafficking motifs that regulate the transport of parasite-encoded proteins across the PV. These articles greatly aid the annotation of the parasite "secretome" catalog of proteins that are targeted to the erythrocyte cytoplasm or cell membrane.

Amino Acid Sequence↗

PubMed2026

Multicellular ecosystems: Linking cellular diversity to tissue function and disease.

Tissue function emerges from coordinated interactions among diverse cell populations, whereas disruption of these interactions can lead to dysfunction. Recent advances in single-cell and spatial genomics have not only cataloged cellular diversity but also revealed how tissues are organized as dynamic multicellular ecosystems. Moving beyond descriptive cell atlases toward functional, system-level representations represents a major frontier in tissue biology. In this review, we outline conceptual and methodological frameworks for dissecting multicellular coordination, highlight recurrent multicellular ecosystems across physiological and pathological contexts, and explore translational opportunities such as patient stratification, therapeutic reprogramming, and regenerative strategies. Viewing tissues through an ecosystem lens provides a unifying framework that links cellular diversity to emergent tissue function and informs strategies for disease intervention.

Humans↗