-
Microbial Ecology Jun 2024Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and...
Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.
Topics: Soil Microbiology; Fagus; Quercus; Forests; Microbiota; Soil; Seasons; Bacteria; Biodiversity; Forestry; Trees; Ecosystem
PubMed: 38940921
DOI: 10.1007/s00248-024-02402-2 -
Physical Chemistry Chemical Physics :... Jun 2024In this work, the ferroelectric and semiconducting properties of the organic semiconducting ferroelectric benzotrithiophene tricarboxamide (BTTTA), and especially their...
In this work, the ferroelectric and semiconducting properties of the organic semiconducting ferroelectric benzotrithiophene tricarboxamide (BTTTA), and especially their nonlinear coupling, are theoretically investigated. BTTTA is an exponent of a small class of semiconducting organic ferroelectrics for which experiments have established a surprising polarization direction dependence of the bulk conductivity at finite fields. First, molecular dynamics (MD) simulations are used to investigate the occurrence and, under the influence of an external electric field, the inversion of the macroscopic electric dipole that forms along the axis of supramolecular columns of BTTTA. The MD results are consistent with the experimentally observed ferroelectric behavior of the material. Building on the MD results, a QM/MM scheme is used to investigate the charge carrier mobility in the quasi-1D BTTTA stacks in the linear and non-linear regimes. Indeed, at finite electric fields, a clear resistance switching effect was observed in the form of a hole mobility that is a factor ∼2 larger for antiparallel orientations of the polarization and field than for a parallel orientation. This phenomenon can be understood as a microscopic ratchet that is based on the non-equilibrium interaction between the (oriented) dipoles and the (direction of the) charge transport.
PubMed: 38940915
DOI: 10.1039/d4cp01632g -
Developmental Dynamics : An Official... Jun 2024Previous studies have claimed that pharyngeal teeth in medaka (Oryzias latipes) are induced independent of retinoic acid (RA) signaling, unlike in zebrafish (Danio...
Differential retinoic acid sensitivity of oral and pharyngeal teeth in medaka (Oryzias latipes) supports the importance of pouch-cleft contacts in pharyngeal tooth initiation.
BACKGROUND
Previous studies have claimed that pharyngeal teeth in medaka (Oryzias latipes) are induced independent of retinoic acid (RA) signaling, unlike in zebrafish (Danio rerio). In zebrafish, pharyngeal tooth formation depends on a proper physical contact between the embryonic endodermal pouch anterior to the site of tooth formation, and the adjacent ectodermal cleft, an RA-dependent process. Here, we test the hypothesis that a proper pouch-cleft contact is required for pharyngeal tooth formation in embryonic medaka, as it is in zebrafish. We used 4-[diethylamino]benzaldehyde (DEAB) to pharmacologically inhibit RA production, and thus pouch-cleft contacts, in experiments strictly controlled in time, and analyzed these using high-resolution imaging.
RESULTS
Pharyngeal teeth in medaka were present only when the corresponding anterior pouch had reached the ectoderm (i.e., a physical pouch-cleft contact established), similar to the situation in zebrafish. Oral teeth were present even when the treatment started approximately 4 days before normal oral tooth appearance.
CONCLUSIONS
RA dependency for pharyngeal tooth formation is not different between zebrafish and medaka. We propose that the differential response to DEAB of oral versus pharyngeal teeth in medaka could be ascribed to the distinct germ layer origin of the epithelia involved in tooth formation in these two regions.
PubMed: 38940489
DOI: 10.1002/dvdy.723 -
Bioinformatics (Oxford, England) Jun 2024Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role...
MOTIVATION
Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role in cellular development, tissue homeostasis, and other critical biological functions. Since direct measurement of CCIs is challenging, multiple methods have been developed to infer CCIs by quantifying correlations between the gene expression of the ligands and receptors that mediate CCIs, originally from bulk RNA-sequencing data and more recently from single-cell or spatially resolved transcriptomics (SRT) data. SRT has a particular advantage over single-cell approaches, since ligand-receptor correlations can be computed between cells or spots that are physically close in the tissue. However, the transcript counts of individual ligands and receptors in SRT data are generally low, complicating the inference of CCIs from expression correlations.
RESULTS
We introduce Copulacci, a count-based model for inferring CCIs from SRT data. Copulacci uses a Gaussian copula to model dependencies between the expression of ligands and receptors from nearby spatial locations even when the transcript counts are low. On simulated data, Copulacci outperforms existing CCI inference methods based on the standard Spearman and Pearson correlation coefficients. Using several real SRT datasets, we show that Copulacci discovers biologically meaningful ligand-receptor interactions that are lowly expressed and undiscoverable by existing CCI inference methods.
AVAILABILITY AND IMPLEMENTATION
Copulacci is implemented in Python and available at https://github.com/raphael-group/copulacci.
Topics: Transcriptome; Cell Communication; Humans; Gene Expression Profiling; Single-Cell Analysis; Algorithms; Computational Biology; Ligands
PubMed: 38940134
DOI: 10.1093/bioinformatics/btae219 -
Journal of Child & Adolescent Trauma Jun 2024PTSD treatment that focused on a sensory symptoms is increasing. The study aimed to explore symptoms and abnormalities in the five senses exhibited by persons with PTSD...
PTSD treatment that focused on a sensory symptoms is increasing. The study aimed to explore symptoms and abnormalities in the five senses exhibited by persons with PTSD and to examine whether there are any differences depending on type of traumatic experience. Questionnaire was followed by interviews to clinical psychologists involved in the treatment of PTSD. 249 PTSD symptoms exhibited in the sensory organs were collected. Sensory symptoms were classified into three categories according to the type of symptoms and the type of traumatic events. Cluster 1 is a group formed by child abuse and violence together with audition, tactile, and hyperarousal. Cluster 2 is made up of natural disaster, accident, and sexual assault together with vision, olfaction and intrusion. Cluster 3 is made up of multiple traumas together with gustation and dissociation. It is speculated that the survivors of Child abuse and violence are hypersensitive to sounds, the presence of others, and physical contact because they try to quickly sense when a perpetrator is approaching. Natural disasters, accidents, and sexual assault are events with strong smell and severe visual impact, it is possible that they may easily cause reliving of the event in the form of shocking visual images and smells in flashbacks. Dissociation symptoms were related with complex trauma and taste. The mouth is the site of first contact between mother and child, and it is possible that gustatory dissociation may occur mainly in cases of severe and repeated trauma since early childhood.
PubMed: 38938954
DOI: 10.1007/s40653-023-00602-5 -
Journal of Child & Adolescent Trauma Jun 2024Unhoused children and adolescents have high rates of adverse childhood experiences (ACEs). The objective of this study was to characterize a large cohort of unhoused...
Unhoused children and adolescents have high rates of adverse childhood experiences (ACEs). The objective of this study was to characterize a large cohort of unhoused children and investigate rates of psychiatric diagnoses, medical diagnoses, and utilization of emergency department (ED) resources depending on the presence of additional documented ACEs. A retrospective cohort of all unhoused children who presented to the ED of a large Midwestern health system from January 2014 to July 2019 were included. Unhoused status was determined by address field or ICD-10 code for homelessness (Z59.0). Demographics and ED visits were extracted from the electronic health record. Past medical history, ACEs, chief complaint (CC), length of stay (LOS), imaging, and labs were extracted by chart review. T-tests, chi square tests, and Fisher's exact tests were completed for each sub-analysis. Unhoused children with at least one additional ACE had higher odds of the following psychiatric disorders: depression (OR = 5.2, 95% CI = 3.4- 7.9), anxiety (OR = 3.4, 95% CI = 32.1-5.5), behavioral disorder (OR = 7.2, 95% CI = 35.1- 10.4), psychoses (OR = 6.0, 1.9-18.4), bipolar disorder (OR = 19.8, 95% CI = 34.6-84.9), suicidal ideation (OR = 8.0, 95% CI = 34.8-13.4), post-traumatic stress disorder (OR = 10.1, 95% CI = 35.4-18.6), and attention deficit hyperactive disorder (OR = 4.1, 3.0-5.7). Patients with additional documented ACEs were also more likely to have a prior psychiatric admission (p < 0.001). Unhoused children and adolescents with exposure to additional documented ACEs are more likely to have some serious psychiatric and medical diagnoses compared to other unhoused children.
PubMed: 38938936
DOI: 10.1007/s40653-023-00608-z -
Essays in Biochemistry Jun 2024The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that...
The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment of their hosts for carbon sources and other nutrients. Metabolic plasticity is crucial to parasite transition between host environments; thus, the regulation of metabolic processes is an important area to explore for therapeutic intervention. Common themes in protozoan parasite metabolism include emphasis on glycolytic catabolism, substrate-level phosphorylation, non-traditional uses of common pathways like tricarboxylic acid cycle and adapted or reduced mitochondria-like organelles. We describe the roles of MDH isoforms in these pathways, discuss unusual structural or functional features of these isoforms relevant to activity or drug targeting, and review current studies exploring the therapeutic potential of MDH and related genes. These studies show that MDH activity has important roles in many metabolic pathways, and thus in the metabolic transitions of protozoan parasites needed for success as pathogens.
PubMed: 38938216
DOI: 10.1042/EBC20230075 -
The American Journal of Chinese Medicine Jun 2024Heat shock proteins (HSPs), which function as chaperones, are activated in response to various environmental stressors. In addition to their role in diverse aspects of...
Heat shock proteins (HSPs), which function as chaperones, are activated in response to various environmental stressors. In addition to their role in diverse aspects of protein production, HSPs protect against harmful protein-related stressors. Calycosin exhibits numerous beneficial properties. This study aims to explore the protective effects of calycosin in the heart under heat shock and determine its underlying mechanism. H9c2 cells, western blot, TUNEL staining, flow cytometry, and immunofluorescence staining were used. The time-dependent effects of heat shock analyzed using western blot revealed increased HSP expression for up to 2[Formula: see text]h, followed by protein degradation after 4[Formula: see text]h. Hence, a heat shock damage duration of 4[Formula: see text]h was chosen for subsequent investigations. Calycosin administered post-heat shock demonstrated dose-dependent recovery of cell viability. Under heat shock conditions, calycosin prevented the apoptosis of H9c2 cells by upregulating HSPs, suppressing p-JNK, enhancing Bcl-2 activation, and inhibiting cleaved caspase 3. Calycosin also inhibited Fas/FasL expression and activated cell survival markers (p-PI3K, p-ERK, p-Akt), indicating their cytoprotective properties through PI3K/Akt activation and JNK inhibition. TUNEL staining and flow cytometry confirmed that calycosin reduced apoptosis. Moreover, calycosin reversed the inhibitory effects of quercetin on HSF1 and Hsp70 expression, illustrating its role in enhancing Hsp70 expression through HSF1 activation during heat shock. Immunofluorescence staining demonstrated HSF1 translocation to the nucleus following calycosin treatment, emphasizing its cytoprotective effects. In conclusion, calycosin exhibits pronounced protective effects against heat shock-induced damages by modulating HSP expression and regulating key signaling pathways to promote cell survival in H9c2 cells.
PubMed: 38938156
DOI: 10.1142/S0192415X24500472 -
Soft Matter Jun 2024Our ability to design artificial micro/nanomachines able to perform sophisticated tasks crucially depends on our understanding of their interaction with biosystems and...
Our ability to design artificial micro/nanomachines able to perform sophisticated tasks crucially depends on our understanding of their interaction with biosystems and their compatibility with the biological environment. Here, we design Janus colloids fuelled only by glucose and light, which can autonomously interact with cell-like compartments and trigger endocytosis. We evidence the crucial role played by the far-field hydrodynamic interaction arising from the puller/pusher swimming mode and adhesion. We show that a large contact time between the active particle and the lipid membrane is required to observe the engulfment of a particle inside a floppy giant lipid vesicle. Active Janus colloids showing relatively small velocities and a puller type swimming mode are able to target giant vesicles, deform their membranes and subsequently get stably engulfed. An instability arising from the unbound membrane segment is responsible for the transition between partial and complete stable engulfment. These experiments shed light on the physical criteria required for autonomous active particle engulfment in giant vesicles, which can serve as general principles in disciplines ranging from drug delivery and microbial infection to nanomedicine.
PubMed: 38938147
DOI: 10.1039/d4sm00337c -
BMC Oral Health Jun 2024To examine the patterns of pretreatment facial soft tissue shape in orthodontic cases with premolar extraction using artificial intelligence (AI) and to investigate the... (Comparative Study)
Comparative Study
OBJECTIVE
To examine the patterns of pretreatment facial soft tissue shape in orthodontic cases with premolar extraction using artificial intelligence (AI) and to investigate the corresponding changes.
METHODS
One hundred and fifty-two patients who underwent orthodontic treatment with premolar extraction were enrolled. Lateral cephalograms were obtained before and after the treatment. For each record, the outlines of the nose-lip-chin profile and corresponding 21 cephalometric variables were extracted. The AI method classified pretreatment records into three subject groups based on the feature variables extracted from the outline. Dentoskeletal and soft tissue facial form changes observed after treatment were compared statistically (P < 0.05) between the groups using ANOVA. Multivariate regression models were used for each group.
RESULTS
Group 1 (n = 59) was characterized by Class II high-angle retrognathic mandible with an incompetent lip, group 2 (n = 55) by Class I malocclusion with retruded and thin lips, and group 3 (n = 38) by Class I malocclusion with an everted superior lip before treatment. The ratios of anteroposterior soft tissue to hard tissue movements in Group 1 were 56% (r = 0.64) and 83% (r = 0.75) for the superior and inferior lips, respectively, whereas those in Group 2 were 49% (r = 0.78) and 91% (r = 0.80), and 40% (r = 0.54) and 79% (r = 0.70), respectively, in Group 3.
CONCLUSIONS
The modes of facial form changes differed depending on the pre-treatment profile patterns classified by the AI. This indicates that the determination of the pre-treatment profile pattern can help in the selection of soft tissue to hard tissue movement ratios, which helps estimate the post-treatment facial profile with a moderate to high correlation.
Topics: Humans; Cephalometry; Face; Bicuspid; Tooth Extraction; Female; Male; Lip; Adolescent; Nose; Malocclusion, Angle Class I; Artificial Intelligence; Chin; Malocclusion, Angle Class II; Mandible; Tooth Movement Techniques; Child; Young Adult; Malocclusion
PubMed: 38937790
DOI: 10.1186/s12903-024-04512-2