EDC-3 and EDC-4 regulate embryonic mRNA clearance and biomolecular condensate specialization.

Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions, but the impact of mRNA decapping scaffold proteins in development is unclear. This study unveils the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including cgh-1, car-1, and ifet-1 by reducing their expression and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a role for EDC-3 in defining the boundaries between P bodies, germ granules, and stress granules. Finally, we show that EDC-4 counteracts EDC-3 and engenders the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings support a model where multiple RNA decay mechanisms temporally clear maternal and zygotic mRNAs throughout embryonic development.

Selective Destabilization of Transcripts by mRNA Decapping Regulates Oocyte Maturation and Innate Immunity Gene Expression during Ageing in C. elegans.

Removal of the 5' cap structure of RNAs (termed decapping) is a pivotal event in the life of cytoplasmic mRNAs mainly catalyzed by a conserved holoenzyme, composed of the catalytic subunit DCP2 and its essential cofactor DCP1. While decapping was initially considered merely a step in the general 5'-3' mRNA decay, recent data suggest a great degree of selectivity that plays an active role in the post-transcriptional control of gene expression, and regulates multiple biological functions. Studies in Caenorhabditis elegans have shown that old age is accompanied by the accumulation of decapping factors in cytoplasmic RNA granules, and loss of decapping activity shortens the lifespan. However, the link between decapping and ageing remains elusive. Here, we present a comparative microarray study that was aimed to uncover the differences in the transcriptome of mid-aged dcap-1/DCP1 mutant and wild-type nematodes. Our data indicate that DCAP-1 mediates the silencing of spermatogenic genes during late oogenesis, and suppresses the aberrant uprise of immunity gene expression during ageing. The latter is achieved by destabilizing the mRNA that encodes the transcription factor PQM-1 and impairing its nuclear translocation. Failure to exert decapping-mediated control on PQM-1 has a negative impact on the lifespan, but mitigates the toxic effects of polyglutamine expression that are involved in human disease.

Immunization with recombinant DcaP-like protein and AbOmpA revealed protections against sepsis infection of multi-drug resistant Acinetobacter baumannii ST2Pas in a C57BL/6 mouse model.

BACKGROUNDS: The prevalence of infections associated with multi-drug resistant (MDR) Acinetobacter baumannii is increasing worldwide. Therefore, the introduction of effective vaccines against this bacterium seems necessary. METHODS: AbOmpA and DcaP-like protein were selected as promising and putative immunogenic candidates based on previous in silico studies. Three formulations including AbOmpA, DcaP-like protein, and AbOmpA + DcaP-like protein were injected into C57BL/6 mice three times with Alum adjuvant. The specific production of IgG antibodies (e.g. total IgG, IgG1 and IgG2c) and cytokines (e.g. IL-4, IL-6, and IL-17A), were evaluated. LD50% of MDR A. baumannii ST2Pas was measured using Probit's method. After the challenge with bacteria, a decrease in bacterial loads (DLs) in the lung and spleen of mice was measured. Then serum bactericidal assay was performed to determine the function of antibodies on day 42. In addition, histopathological examinations of the spleen and lung, the number of macrophage and neutrophil, as well as the rate of lymphocyte infiltration were assessed. RESULTS: The highest level of total IgG was reported in the group immunized with DcaP-like protein on day 42. The survival rate of mice was 80% in the AbOmpA immunized group and 100% for the rest of two groups. DLs in the spleen of mice immunized with AbOmpA, DcaP-like protein, and combination form were 3.5, 3, and 3.4 Log10 (CFU/g), respectively. While in the lung, the DLs were 7.5 Log10 (CFU/g) for the AbOmpA group and 5 for the rest of two groups. The levels of IL-6, IL-4, and IL-17A were significantly decreased in all immunized groups after the bacterial challenge (except for IL-17A in the group of AbOmpA). The bactericidal effect of antibodies against DcaP-like protein was more effective. No histopathological damage was observed in the combination immunized group. The DcaP-like protein was more effective in neutrophil and macrophage deployment and decreased lymphocyte infiltration. CONCLUSION: The results of immunization with AbOmpA + DcaP-like protein induced a protective reaction against the sepsis infection of MDR A. baumannii. It seems that in the future, these proteins can be considered as promising components in the development of the A. baumannii vaccine.

Novel QTL for Low Seed Cadmium Accumulation in Soybean.

Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg-1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1.

DcaP porin and its epitope-based subunit promise effective vaccines against Acinetobacter baumannii; in-silico and in-vivo approaches.

A. baumannii is a multi-drug resistant pathogen with a relatively high mortality rate. To date, no vaccine has been approved against this bacterium. DcaP is a high abundance porin during infection that its structure has been recently determined, but no information about its immunogenic properties has been reported yet. So, in this study DcaP properties were analyzed and its vaccine potential was evaluated. The results showed this porin is an extremely conserved antigen with no allergenicity and toxicity that bears no resemblance to human proteins. Six potential immunogen areas in the DcaP sequence were detected based on in-silico B and T-cell epitope mapping and other approaches. A multiple-epitope potential vaccine was designed based on the predicted linear epitopes and amplified by overlap extension PCR technique. In-vivo results indicated that active and passive immunization of mice with the DcaP protein or its designed subunit vaccine raises the antibody titers and decreases the mortality rate of the immunized mice infected with A. baumannii. Based on the results, DcaP and its indicated immunogen regions can be considered as a peptide or subunit vaccine. The immunogen regions could also be applied in multivalent subunit vaccine candidates against A. baumannii and other bacteria.

Signaling by AWC Olfactory Neurons Is Necessary for Caenorhabditis elegans' Response to Prenol, an Odor Associated with Nematode-Infected Insects.

Chemosensation plays a role in the behaviors and life cycles of numerous organisms, including nematodes. Many guilds of nematodes exist, ranging from the free-living Caenorhabditis elegans to various parasitic species such as entomopathogenic nematodes (EPNs), which are parasites of insects. Despite ecological differences, previous research has shown that both EPNs and C. elegans respond to prenol (3-methyl-2-buten-1-ol), an odor associated with EPN infections. However, it is unclear how C. elegans responds to prenol. By utilizing natural variation and genetic neuron ablation to investigate the response of C. elegans to prenol, we found that the AWC neurons are involved in the detection of prenol and that several genes (including dcap-1, dcap-2, and clec-39) influence response to this odorant. Furthermore, we identified that the response to prenol is mediated by the canonically proposed pathway required for other AWC-sensed attractants. However, upon testing genetically diverse isolates, we found that the response of some strains to prenol differed from their response to isoamyl alcohol, suggesting that the pathways mediating response to these two odorants may be genetically distinct. Further, evaluations leveraging natural variation and genome wide association revealed specific genes that influence nematode behavior and provide a foundation for future studies to better understand the role of prenol in nematode behavioral ecology.

mRNA decapping is an evolutionarily conserved modulator of neuroendocrine signaling that controls development and ageing.

Eukaryotic 5'-3' mRNA decay plays important roles during development and in response to stress, regulating gene expression post-transcriptionally. In Caenorhabditis elegans, deficiency of DCAP-1/DCP1, the essential co-factor of the major cytoplasmic mRNA decapping enzyme, impacts normal development, stress survival and ageing. Here, we show that overexpression of dcap-1 in neurons of worms is sufficient to increase lifespan through the function of the insulin/IGF-like signaling and its effector DAF-16/FOXO transcription factor. Neuronal DCAP-1 affects basal levels of INS-7, an ageing-related insulin-like peptide, which acts in the intestine to determine lifespan. Short-lived dcap-1 mutants exhibit a neurosecretion-dependent upregulation of intestinal ins-7 transcription, and diminished nuclear localization of DAF-16/FOXO. Moreover, neuronal overexpression of DCP1 in Drosophila melanogaster confers longevity in adults, while neuronal DCP1 deficiency shortens lifespan and affects wing morphogenesis, cell non-autonomously. Our genetic analysis in two model-organisms suggests a critical and conserved function of DCAP-1/DCP1 in developmental events and lifespan modulation.

Mapping a double flower phenotype-associated gene DcAP2L in Dianthus chinensis.

The double flower is a highly important breeding trait that affects the ornamental value in many flowering plants. To get a better understanding of the genetic mechanism of double flower formation in Dianthus chinensis, we have constructed a high-density genetic map using 140 F2 progenies derived from a cross between a single flower genotype and a double flower genotype. The linkage map was constructed using double-digest restriction site-associated DNA sequencing (ddRAD-seq) with 2353 single nucleotide polymorphisms (SNPs). Quantitative trait locus (QTL) mapping analysis was conducted for 12 horticultural traits, and major QTLs were identified for nine of the 12 traits. Among them, two major QTLs accounted for 20.7% and 78.1% of the total petal number variation, respectively. Bulked segregant RNA-seq (BSR-seq) was performed to search accurately for candidate genes associated with the double flower trait. Integrative analysis of QTL mapping and BSR-seq analysis using the reference genome of Dianthus caryophyllus suggested that an SNP mutation in the miR172 cleavage site of the A-class flower organ identity gene APETALA2 (DcAP2L) is responsible for double flower formation in Dianthus through regulating the expression of DcAG genes.

A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii.

Research efforts to discover potential new antibiotics for Gram-negative bacteria suffer from high attrition rates due to the synergistic action of efflux systems and the limited permeability of the outer membrane (OM). One strategy to overcome the OM permeability barrier is to identify small molecules that are natural substrates for abundant OM channels and use such compounds as scaffolds for the design of efficiently permeating antibacterials. Here we present a multidisciplinary approach to identify such potential small-molecule scaffolds. Focusing on the pathogenic bacterium Acinetobacter baumannii, we use OM proteomics to identify DcaP as the most abundant channel during infection in rodents. The X-ray crystal structure of DcaP reveals a trimeric, porin-like structure and suggests that dicarboxylic acids are potential transport substrates. Electrophysiological experiments and all-atom molecular dynamics simulations confirm this notion and provide atomistic information on likely permeation pathways and energy barriers for several small molecules, including a clinically relevant ß-lactamase inhibitor.

Incorporating spatial constraint in co-activation pattern analysis to explore the dynamics of resting-state networks: An application to Parkinson's disease.

The dynamics of the brain's intrinsic networks have been recently studied using co-activation pattern (CAP) analysis. The CAP method relies on few model assumptions and CAP-based measurements provide quantitative information of network temporal dynamics. One limitation of existing CAP-related methods is that the computed CAPs share considerable spatial overlap that may or may not be functionally distinct relative to specific network dynamics. To more accurately describe network dynamics with spatially distinct CAPs, and to compare network dynamics between different populations, a novel data-driven CAP group analysis method is proposed in this study. In the proposed method, a dominant-CAP (d-CAP) set is synthesized across CAPs from multiple clustering runs for each group with the constraint of low spatial similarities among d-CAPs. Alternating d-CAPs with less overlapping spatial patterns can better capture overall network dynamics. The number of d-CAPs, the temporal fraction and spatial consistency of each d-CAP, and the subject-specific switching probability among all d-CAPs are then calculated for each group and used to compare network dynamics between groups. The spatial dissimilarities among d-CAPs computed with the proposed method were first demonstrated using simulated data. High consistency between simulated ground-truth and computed d-CAPs was achieved, and detailed comparisons between the proposed method and existing CAP-based methods were conducted using simulated data. In an effort to physiologically validate the proposed technique and investigate network dynamics in a relevant brain network disorder, the proposed method was then applied to data from the Parkinson's Progression Markers Initiative (PPMI) database to compare the network dynamics in Parkinson's disease (PD) and normal control (NC) groups. Fewer d-CAPs, skewed distribution of temporal fractions of d-CAPs, and reduced switching probabilities among final d-CAPs were found in most networks in the PD group, as compared to the NC group. Furthermore, an overall negative association between switching probability among d-CAPs and disease severity was observed in most networks in the PD group as well. These results expand upon previous findings from in vivo electrophysiological recording studies in PD. Importantly, this novel analysis also demonstrates that changes in network dynamics can be measured using resting-state fMRI data from subjects with early stage PD.

Neuronal function of the mRNA decapping complex determines survival of Caenorhabditis elegans at high temperature through temporal regulation of heterochronic gene expression.

In response to adverse environmental cues, Caenorhabditis elegans larvae can temporarily arrest development at the second moult and form dauers, a diapause stage that allows for long-term survival. This process is largely regulated by certain evolutionarily conserved signal transduction pathways, but it is also affected by miRNA-mediated post-transcriptional control of gene expression. The 5'-3' mRNA decay mechanism contributes to miRNA-mediated silencing of target mRNAs in many organisms but how it affects developmental decisions during normal or stress conditions is largely unknown. Here, we show that loss of the mRNA decapping complex activity acting in the 5'-3' mRNA decay pathway inhibits dauer formation at the stressful high temperature of 27.5°C, and instead promotes early developmental arrest. Our genetic data suggest that this arrest phenotype correlates with dysregulation of heterochronic gene expression and an aberrant stabilization of lin-14 mRNA at early larval stages. Restoration of neuronal dcap-1 activity was sufficient to rescue growth phenotypes of dcap-1 mutants at both high and normal temperatures, implying the involvement of common developmental timing mechanisms. Our work unveils the crucial role of 5'-3' mRNA degradation in proper regulation of heterochronic gene expression programmes, which proved to be essential for survival under stressful conditions.

Drosophila Condensin II subunit Chromosome-associated protein D3 regulates cell fate determination through non-cell-autonomous signaling.

The pattern of the Drosophila melanogaster adult wing is heavily influenced by the expression of proteins that dictate cell fate decisions between intervein and vein during development. dSRF (Blistered) expression in specific regions of the larval wing disc promotes intervein cell fate, whereas EGFR activity promotes vein cell fate. Here, we report that the chromatin-organizing protein CAP-D3 acts to dampen dSRF levels at the anterior/posterior boundary in the larval wing disc, promoting differentiation of cells into the anterior crossvein. CAP-D3 represses KNOT expression in cells immediately adjacent to the anterior/posterior boundary, thus blocking KNOT-mediated repression of EGFR activity and preventing cell death. Maintenance of EGFR activity in these cells depresses dSRF levels in the neighboring anterior crossvein progenitor cells, allowing them to differentiate into vein cells. These findings uncover a novel transcriptional regulatory network influencing Drosophila wing vein development, and are the first to identify a Condensin II subunit as an important regulator of EGFR activity and cell fate determination in vivo.

Validation of the dementia care assessment packet-instrumental activities of daily living.

OBJECTIVE: We aimed to evaluate the psychometric properties of the IADL measure included in the Dementia Care Assessment Packet (DCAP-IADL) in dementia patients. METHODS: The study involved 112 dementia patients and 546 controls. The DCAP-IADL was scored in two ways: observed score (OS) and predicted score (PS). The reliability of the DCAP-IADL was evaluated by testing its internal consistency, inter-rater reliability and test-retest reliability. Discriminant validity was evaluated by comparing the mean OS and PS between dementia patients and controls by ANCOVA. Pearson or Spearman correlation analysis was performed with other instruments to assess concurrent validity. Receiver operating characteristics curve analysis was performed to examine diagnostic accuracy. RESULTS: Chronbach's α coefficients of the DCAP-IADL were above 0.7. The values in dementia patients were much higher (OS=0.917, PS=0.927), indicating excellent degrees of internal consistency. Inter-rater reliabilities and test-retest reliabilities were statistically significant (p<0.05). PS exhibited higher reliabilities than OS. The mean OS and PS of dementia patients were significantly higher than those of the non-demented group after controlling for age, sex and education level. The DCAP-IADL was significantly correlated with other IADL instruments and MMSE-KC (p<0.001). Areas under the curves of the DCAP-IADL were above 0.9. CONCLUSION: The DCAP-IADL is a reliable and valid instrument for evaluating instrumental ability of daily living for the elderly, and may also be useful for screening dementia. Moreover, administering PS may enable the DCAP-IADL to overcome the differences in gender, culture and life style that hinders accurate evaluation of the elderly in previous IADL instruments.

Validation of the Dementia Care Assessment Packet-Instrumental Activities of Daily Living

OBJECTIVE: We aimed to evaluate the psychometric properties of the IADL measure included in the Dementia Care Assessment Packet (DCAP-IADL) in dementia patients. METHODS: The study involved 112 dementia patients and 546 controls. The DCAP-IADL was scored in two ways: observed score (OS) and predicted score (PS). The reliability of the DCAP-IADL was evaluated by testing its internal consistency, inter-rater reliability and test-retest reliability. Discriminant validity was evaluated by comparing the mean OS and PS between dementia patients and controls by ANCOVA. Pearson or Spearman correlation analysis was performed with other instruments to assess concurrent validity. Receiver operating characteristics curve analysis was performed to examine diagnostic accuracy. RESULTS: Chronbach's alpha coefficients of the DCAP-IADL were above 0.7. The values in dementia patients were much higher (OS=0.917, PS=0.927), indicating excellent degrees of internal consistency. Inter-rater reliabilities and test-retest reliabilities were statistically significant (p<0.05). PS exhibited higher reliabilities than OS. The mean OS and PS of dementia patients were significantly higher than those of the non-demented group after controlling for age, sex and education level. The DCAP-IADL was significantly correlated with other IADL instruments and MMSE-KC (p<0.001). Areas under the curves of the DCAP-IADL were above 0.9. CONCLUSION: The DCAP-IADL is a reliable and valid instrument for evaluating instrumental ability of daily living for the elderly, and may also be useful for screening dementia. Moreover, administering PS may enable the DCAP-IADL to overcome the differences in gender, culture and life style that hinders accurate evaluation of the elderly in previous IADL instruments.