MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints.

MOTIVATION: Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts in molecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios. RESULTS: Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates. AVAILABILITY AND IMPLEMENTATION: The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA.

Mobile Host mRNAs Are Translated to Protein in the Associated Parasitic Plant Cuscuta campestris.

Cuscuta spp. are obligate parasites that connect to host vascular tissue using a haustorium. In addition to water, nutrients, and metabolites, a large number of mRNAs are bidirectionally exchanged between Cuscuta spp. and their hosts. This trans-specific movement of mRNAs raises questions about whether these molecules function in the recipient species. To address the possibility that mobile mRNAs are ultimately translated, we built upon recent studies that demonstrate a role for transfer RNA (tRNA)-like structures (TLSs) in enhancing mRNA systemic movement. C. campestris was grown on Arabidopsis that expressed a ß-glucuronidase (GUS) reporter transgene either alone or in GUS-tRNA fusions. Histochemical staining revealed localization in tissue of C. campestris grown on Arabidopsis with GUS-tRNA fusions, but not in C. campestris grown on Arabidopsis with GUS alone. This corresponded with detection of GUS transcripts in Cuscuta on Arabidopsis with GUS-tRNA, but not in C. campestris on Arabidopsis with GUS alone. Similar results were obtained with Arabidopsis host plants expressing the same constructs containing an endoplasmic reticulum localization signal. In C. campestris, GUS activity was localized in the companion cells or phloem parenchyma cells adjacent to sieve tubes. We conclude that host-derived GUS mRNAs are translated in C. campestris and that the TLS fusion enhances RNA mobility in the host-parasite interactions.

Multiple immunity-related genes control susceptibility of Arabidopsis thaliana to the parasitic weed Phelipanche aegyptiaca.

Parasitic weeds represent a major threat to agricultural production across the world. Little is known about which host genetic pathways determine compatibility for any host-parasitic plant interaction. We developed a quantitative assay to characterize the growth of the parasitic weed Phelipanche aegyptiaca on 46 mutant lines of the host plant Arabidopsis thaliana to identify host genes that are essential for susceptibility to the parasite. A. thaliana host plants with mutations in genes involved in jasmonic acid biosynthesis/signaling or the negative regulation of plant immunity were less susceptible to P. aegyptiaca parasitization. In contrast, A. thaliana plants with a mutant allele of the putative immunity hub gene Pfd6 were more susceptible to parasitization. Additionally, quantitative PCR revealed that P. aegyptiaca parasitization leads to transcriptional reprograming of several hormone signaling pathways. While most tested A. thaliana lines were fully susceptible to P. aegyptiaca parasitization, this work revealed several host genes essential for full susceptibility or resistance to parasitism. Altering these pathways may be a viable approach for limiting host plant susceptibility to parasitism.

Bypassing miRNA-mediated gene regulation under drought stress: alternative splicing affects CSD1 gene expression.

KEY MESSAGE: The binding site for miR398 in an isoform of Cu/Zn superoxide dismutase (CSD1) is eliminated by alternative splicing to bypass miR398-mediated gene down-regulation under drought stress. MicroRNA (miRNA) binding sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generate functional MBSs in target transcripts. MBSs can also be excluded during splicing of pre-messenger RNA, leading to different regulation among isoforms. Previous studies have shown that levels of Cu/Zn superoxide dismutase (CSD) are down-regulated by miR398. In this study, sequences and transcript levels of peanut CSD1 isoforms (AhCSD1-1, AhCSD1-2.1, and AhCSD1-2.2) were analyzed under the drought stress. Results demonstrated that a miR398 binding site is eliminated in AhCSD1-2.2 as a consequence of alternative splicing, which bypasses miRNA-mediated down-regulation under drought stress. This alternative isoform was not only identified in peanut but also in soybean and Arabidopsis. In addition, transgenic Arabidopsis plants expressing AhCSD1 were more tolerant to osmotic stress. We hypothesize that the level of AhCSD1 is increased to allow diverse plant responses to overcome environmental challenges even in the presence of increased miR398 levels. These findings suggest that studies on the role of alternatively spliced MBSs affecting transcript levels are important for understanding plant stress responses.

Chemokine in inflamed periodontal tissues activates healthy periodontal-ligament stem cell migration.

AIM: The present study aimed to characterize the expression pattern of chemokines obtained from inflamed periodontal defects and to determine the characteristics of human periodontal-ligament stem cells (hPDLSCs) migrated by each specific chemokine. MATERIALS AND METHODS: Both inflamed and healthy periodontal tissues were obtained from periodontitis patients (n = 11), and the chemokine expression levels were analyzed. The periodontal-tissue-specific chemokines were applied to healthy hPDLSCs from extracted teeth (n = 3), with FGF-2 acting as a positive control. Cells were separated by selected chemokines using transwell method into migrated/unmigrated hPDLSCs. The characteristics of the hPDLSC subpopulation recruited by each chemokine were assessed, and gene expression pattern was analyzed by microarray. RESULTS: Chemokines were categorized into three groups by specific patterns of "appearing," "increasing," and "decreasing/disappearing" from healthy to inflamed tissues. A representative chemokine from each group enhanced the capacities for colony formation and osteogenic/adipogenic differentiation while maintaining the surface markers of hPDLSCs. RANTES/CCL5 significantly increased the cellular migration of hPDLSCs, via enhancement of signaling pathways, regulation of the actin skeleton, and focal adhesion. CONCLUSION: The present study found a specific chemokine profile induced by inflammation in periodontal tissues, with RANTES/CCL5 appearing to play a role in the migration of hPDLSCs into inflammatory periodontal lesions.

Differential isoform expression and protein localization from alternatively spliced Apetala2 in peanut under drought stress.

APETALA2 (AP2) belongs to the AP2/Ethylene Responsive Factor (ERF) family and regulates expression levels of downstream stress responsive genes as a transcription factor. In this study, we cloned six different isoforms of AhAP2 from peanut (Arachis hypogaea). Four isoforms (AhAP2.1, AhAP2.2, AhAP2.3 and AhAP2.4) had both AP2/ERF DNA binding domains and ERF-associated amphiphilic repression (EAR) motifs. Two isoforms (AhAP2.5 and AhAP2.6) only had an EAR suppressor domain. After agroinfiltration, AhAP2.1, AhAP2.3, and AhAP2.4 fused to yellow fluorescent protein (YFP) showed localization to the nucleolus, which is the site of transcription and ribosome biogenesis. AhAP2.2-YFP showed a dispersed signal in the nucleus. AhAP2.5 and AhAP2.6 fused to YFP localized to both the nucleus and cytoplasm. In addition, increased levels of AhAP2.1 and AhAP2.2 transcripts were observed in drought-treated peanut leaves, suggesting differential transcriptional regulation under drought stress conditions.

Gene Silencing and Haploinsufficiency of Csk Increase Blood Pressure.

OBJECTIVE: Recent genome-wide association studies have identified 33 human genetic loci that influence blood pressure. The 15q24 locus is one such locus that has been confirmed in Asians and Europeans. There are 21 genes in the locus within a 1-Mb boundary, but a functional link of these genes to blood pressure has not been reported. We aimed to identify a causative gene for blood pressure change in the 15q24 locus. METHODS AND RESULTS: CSK and ULK3 were selected as candidate genes based on eQTL analysis studies that showed the association between gene transcript levels and the lead SNP (rs1378942). Injection of siRNAs for mouse homologs Csk, Ulk3, and Cyp1a2 (negative control) showed reduced target gene mRNA levels in vivo. However, Csk siRNA only increased blood pressure while Ulk3 and Cyp1a2 siRNA did not change it. Further, blood pressure in Csk+/- heterozygotes was higher than in wild-type, consistent with what we observed in Csk siRNA-injected mice. We confirmed that haploinsufficiency of Csk increased the active form of Src in Csk+/- mice aorta. We also showed that inhibition of Src by PP2, a Src inhibitor decreased high blood pressure in Csk+/- mice and the active Src in Csk+/- mice aorta and in Csk knock-down vascular smooth muscle cells, suggesting blood pressure regulation by Csk through Src. CONCLUSIONS: Our study demonstrates that Csk is a causative gene in the 15q24 locus and regulates blood pressure through Src, and these findings provide a novel therapeutic target for the treatment of hypertension.

In vivo bone formation by human alveolar-bone-derived mesenchymal stem cells obtained during implant osteotomy using biphasic calcium phosphate ceramics or Bio-Oss as carriers.

OBJECTIVES: The aim of this study was to evaluate HA coated with different ratios of TCP as a carrier for hABMSCs obtained during implant osteotomy in comparison to slowly-resorbing biomaterial, Bio-Oss, as a negative control, using in vitro and in vivo experiments. MATERIALS AND METHODS: Human ABMSCs (hABMSCs) harvested during implant osteotomy were transplanted using HA/TCP or Bio-Oss as carriers in a murine ectopic transplantation model (n = 12). Pore size and cell affinity were evaluated in vitro. The area of newly formed bone was analyzed histometrically, the number of osteocytes was counted, and immunohistochemical staining was conducted against several markers of osteogenesis, including alkaline phosphatase (ALP), runt-related transcription factor 2 (RUNX-2), osteocalcin (OCN), and osteopontin (OPN). Osteoclast formation was evaluated by tartrate-resistant acid phosphatase staining. RESULTS: The carrier materials had comparable pore sizes. The cell affinity assay resulted in a high proportion of cell adhesion (>90%) in all experimental groups. Substantial new bone and osteocyte formation was observed on both HA/TCP carriers, whereas it was minimal with Bio-Oss. Positive immunostaining for ALP, RUNX-2, OCN, and OPN was observed with HA/TCP, but only limited expression of osteogenic markers with Bio-Oss. Conversely, there was a minimal osteoclast presence with Bio-Oss, but a significant presence of osteoclasts with both HA/TCP carriers. CONCLUSIONS: Both types of scaffolds, BCP and Bio-Oss, showed high stem cell-carrying potential, but the in vivo healing patterns of their complexes with hABMSC could be affected by the microenvironment on the surfaces of the scaffolds.

Human bone marrow stem cells cultured under hypoxic conditions present altered characteristics and enhanced in vivo tissue regeneration.

Human bone marrow mesenchymal stem cells (hBMSCs) were isolated from bone marrow of the vertebral body. The hBMSCs were cultured under either hypoxic (1% O2) or normoxic (21% O2; control) conditions and the characteristics as mesenchymal stem cells were compared. Results revealed that hypoxia reduced proliferative potential and colony-forming efficiency of hBMSCs, and significantly enhanced osteogenic and chondrogenic differentiation. The hBMSCs enhanced the regenerative potential of bone in vivo. In vitro synthesis of soluble and insoluble collagen was significantly increased in the hypoxic condition. In vivo collagen tissue regeneration was also enhanced under the hypoxic condition, with concomitant increased expressions of various subtypes of collagen and lysyl-oxidase family mRNA. MicroRNA assays revealed that miR-155-5p, which negatively regulates HIF-1α, was significantly highly expressed. These observations demonstrate that hBMSCs obtained from human vertebrae exhibit altered characteristics under hypoxic conditions, and each factor contributing to hBMSC-mediated tissue healing should be evaluated with the goal of allowing their clinical application.

The Divergent Roles of STAYGREEN (SGR) Homologs in Chlorophyll Degradation.

Degradation of chlorophyll (Chl) by Chl catabolic enzymes (CCEs) causes the loss of green color that typically occurs during senescence of leaves. In addition to CCEs, staygreen1 (SGR1) functions as a key regulator of Chl degradation. Although sgr1 mutants in many plant species exhibit a stay-green phenotype, the biochemical function of the SGR1 protein remains elusive. Many recent studies have examined the physiological and molecular roles of SGR1 and its homologs (SGR2 and SGR-LIKE) in Chl metabolism, finding that these proteins have different roles in different species. In this review, we summarize the recent studies on SGR and discuss the most likely functions of SGR homologs.

Agrobacterium T-DNA integration into the plant genome can occur without the activity of key non-homologous end-joining proteins.

Non-homologous end joining (NHEJ) is the major model proposed for Agrobacterium T-DNA integration into the plant genome. In animal cells, several proteins, including KU70, KU80, ARTEMIS, DNA-PKcs, DNA ligase IV (LIG4), Ataxia telangiectasia mutated (ATM), and ATM- and Rad3-related (ATR), play an important role in 'classical' (c)NHEJ. Other proteins, including histone H1 (HON1), XRCC1, and PARP1, participate in a 'backup' (b)NHEJ process. We examined transient and stable transformation frequencies of Arabidopsis thaliana roots mutant for numerous NHEJ and other related genes. Mutants of KU70, KU80, and the plant-specific DNA Ligase VI (LIG6) showed increased stable transformation susceptibility. However, these mutants showed transient transformation susceptibility similar to that of wild-type plants, suggesting enhanced T-DNA integration in these mutants. These results were confirmed using a promoter-trap transformation vector that requires T-DNA integration into the plant genome to activate a promoterless gusA (uidA) gene, by virus-induced gene silencing (VIGS) of Nicotiana benthamiana NHEJ genes, and by biochemical assays for T-DNA integration. No alteration in transient or stable transformation frequencies was detected with atm, atr, lig4, xrcc1, or parp1 mutants. However, mutation of parp1 caused high levels of T-DNA integration and transgene methylation. A double mutant (ku80/parp1), knocking out components of both NHEJ pathways, did not show any decrease in stable transformation or T-DNA integration. Thus, T-DNA integration does not require known NHEJ proteins, suggesting an alternative route for integration.

Reduction of Adipose Tissue Formation by the Controlled Release of BMP-2 Using a Hydroxyapatite-Coated Collagen Carrier System for Sinus-Augmentation/Extraction-Socket Grafting.

The effects of hydroxyapatite (HA)-coating onto collagen carriers for application of recombinant human bone morphogenetic protein 2 (rhBMP-2) on cell differentiation in vitro, and on in vivo healing patterns after sinus-augmentation and alveolar socket-grafting were evaluated. In vitro induction of osteogenic/adipogenic differentiation was compared between the culture media with rhBMP-2 solution and with the released rhBMP-2 from the control collagen and from the HA-coated collagen. Demineralized bovine bone and collagen/HA-coated collagen were grafted with/without rhBMP-2 in sinus-augmentation and tooth-extraction-socket models. Adipogenic induction by rhBMP-2 released from HA-coated collagen was significantly reduced compared to collagen. In the sinus-augmentation model, sites that received rhBMP-2 exhibited large amounts of vascular tissue formation at two weeks and increased adipose tissue formation at eight weeks; this could be significantly reduced by using HA-coated collagen as a carrier for rhBMP-2. In extraction-socket grafting, dimensional reduction of alveolar ridge was significantly decreased at sites received rhBMP-2 compared to control sites, but adipose tissue was increased within the regenerated socket area. In conclusion, HA-coated collagen carrier for Escherichia coli-derived rhBMP-2 (ErhBMP-2) may reduce in vitro induction of adipogenic differentiation and in vivo adipose bone marrow tissue formation in bone tissue engineering by ErhBMP-2.

Synergistic Effects of a Calcium Phosphate/Fibronectin Coating on the Adhesion of Periodontal Ligament Stem Cells Onto Decellularized Dental Root Surfaces.

This study aimed to enhance the attachment of periodontal ligament stem cells (PDLSCs) onto the decellularized dental root surface using surface coating with fibronectin and/or calcium phosphate (CaP) and to evaluate the activity of PDLSCs attached to a coated dental root surface following tooth replantation. PDLSCs were isolated from five dogs, and the other dental roots were used as a scaffold for carrying PDLSCs and then assigned to one of four groups according to whether their surface was coated with CaP, fibronectin, CaP/fibronectin, or left uncoated (control). Fibronectin increased the adhesion of PDLSCs onto dental root surfaces compared to both the control and CaP-coated groups, and simultaneous surface coating with CaP and fibronectin significantly accelerated and increased PDLSC adhesion compared to the fibronectin-only group. On in vivo tooth replantation, functionally oriented periodontal new attachment was observed on the CaP/fibronectin-coated dental roots to which autologous PDLSCs had adhered, while in the control condition, dental root replantation was associated only with root resorption and ankylosis along the entire root length. CaP and fibronectin synergistically enhanced the attachment of PDLSCs onto dental root surfaces, and autologous PDLSCs could produce de novo periodontal new attachment in an experimental in vivo model.

Effect of FGF-2 on collagen tissue regeneration by human vertebral bone marrow stem cells.

The effects of fibroblast growth factor-2 (FGF-2) on collagen tissue regeneration by human bone marrow stem cells (hBMSCs) were investigated. hBMSCs were isolated from human vertebral body bone marrow during vertebral surgery and a population of hBMSCs with the characteristics of mesenchymal stem cells was observed. The FGF-2 treatment (5 ng/mL) affected on the colony-forming efficiency, proliferation, and in vitro differentiation of hBMSCs. Insoluble/soluble collagen and hydroxyproline synthesis was significantly enhanced in hBMSCs expanded with FGF-2 and the treatment of FGF-2 caused a reduction in the mRNA expression of collagen type I, but an increase of collagen types II and III along with lysyl oxidase family genes. Collagen formation was also examined using an in vivo assay model by transplanting hBMSCs into immunocompromised mice (n=4) and the histologic and immunohistochemical results revealed that significantly more collagen with a well-organized structure was formed by FGF-2-treated hBMSCs at 8 weeks posttransplantation (P<0.05). The DNA microarray assay demonstrated that genes related to extracellular matrix formation were significantly upregulated. To elucidate the underlying mechanism, chemical inhibitors against extracellular-signal-regulated kinase (ERK) and phosphoinositide 3-kinase (PI3K) were treated and following downstream expression was observed. Collectively, FGF-2 facilitated the collagen-producing potency of hBMSCs both in vitro and in vivo, rendering them more suitable for use in collagen regeneration in the clinical field.

Differential effect of water-soluble chitin on collagen synthesis of human bone marrow stem cells and human periodontal ligament stem cells.

Human bone marrow stem cells (hBMSCs) represent a promising regenerative material because of their mutipotency, including their ability to regenerate collagenous soft tissues. We previously found that water-soluble chitin (WSC) enhances the ability of human periodontal ligament stem cells (hPDLSCs) to synthesize collagen tissue. The aim of this study was to determine the effects of WSC on hBMSCs and hPDLSCs for the collagen synthesis both in vitro and in vivo. hBMSCs and hPDLSCs were isolated and expanded with or without 0.3 mg/mL WSC. A series of in vitro and in vivo analyses were performed to evaluate their characteristics as stem cell populations. Then, collagen and hydroxyproline assays were conducted using both in vitro and in vivo assay models, and the real-time polymerase chain reaction was performed to analyze the expression of collagen-related markers. WSC-treated and nontreated hBMSCs and hPDLSCs were transplanted into immunocompromised mice, and histology and immunohistochemistry analyses were conducted after 8 weeks. The in vitro results showed that those cells possessed the characteristics of mesenchymal stem cells. The amount of soluble collagen synthesized was significantly greater in WSC-treated hBMSCs than in the nontreated group; conversely, treatment of hPDLSCs with WSC decreased the formation of soluble collagen. The amount of insoluble collagen synthesized was greater in the WSC-treated groups than in the nontreated groups for both hBMSCs and hPDLSCs. The hydroxyproline contents of the regenerated soluble and insoluble collagens were similar. The expressions of mRNA for collagen types I-V, hyaluronic acid synthase 1 (HAS1), HAS2, and HAS3, and the LOX family were higher in WSC-treated hPDLSCs than in the nontreated group, whereas WSC increased the expression of collagen type III and decreased that of collagen type I in hBMSCs. The histology and immunohistochemistry results revealed that WSC significantly increased the amount of collagen formed in vivo by both types of stem cells. Collectively, treatment with WSC significantly enhanced the collagen-forming potentials of hBMSCs and hPDLSCs, but the collagen they produced exhibited distinctively different characteristics. These findings suggest that the appropriate stem-cell source should be chosen based on the purpose of the required regenerated tissue.

Arabidopsis STAY-GREEN2 is a negative regulator of chlorophyll degradation during leaf senescence.

Chlorophyll (Chl) degradation causes leaf yellowing during senescence or under stress conditions. For Chl breakdown, STAY-GREEN1 (SGR1) interacts with Chl catabolic enzymes (CCEs) and light-harvesting complex II (LHCII) at the thylakoid membrane, possibly to allow metabolic channeling of potentially phototoxic Chl breakdown intermediates. Among these Chl catabolic components, SGR1 acts as a key regulator of leaf yellowing. In addition to SGR1 (At4g22920), the Arabidopsis thaliana genome contains an additional homolog, SGR2 (At4g11910), whose biological function remains elusive. Under senescence-inducing conditions, SGR2 expression is highly up-regulated, similarly to SGR1 expression. Here we show that SGR2 function counteracts SGR1 activity in leaf Chl degradation; SGR2-overexpressing plants stayed green and the sgr2-1 knockout mutant exhibited early leaf yellowing under age-, dark-, and stress-induced senescence conditions. Like SGR1, SGR2 interacted with LHCII but, in contrast to SGR1, SGR2 interactions with CCEs were very limited. Furthermore, SGR1 and SGR2 formed homo- or heterodimers, strongly suggesting a role for SGR2 in negatively regulating Chl degradation by possibly interfering with the proposed CCE-recruiting function of SGR1. Our data indicate an antagonistic evolution of the functions of SGR1 and SGR2 in Arabidopsis to balance Chl catabolism in chloroplasts with the dismantling and remobilizing of other cellular components in senescing leaf cells.

Silencing of Atp2b1 increases blood pressure through vasoconstriction.

BACKGROUND: Recent genome-wide association studies (GWASs) have identified 30 genetic loci that regulate blood pressure, increasing our understanding of the cause of hypertension. However, it has been difficult to define the causative genes at these loci due to a lack of functional analyses. METHOD: In this study, we aimed to validate the candidate gene ATP2B1 in 12q21, variants near which have the strongest association with blood pressure in Asians and Europeans. ATP2B1 functions as a calcium pump to fine-tune calcium concentrations - necessary for repolarization following muscular contractions. We silenced Atp2b1 using an siRNA complex, injected into mouse tail veins. RESULTS: In treated mice, blood pressure rose and the mesenteric arteries increased in wall : lumen ratio. Moreover, the arteries showed enhanced myogenic responses to pressure, and contractile responses to phenylephrine increased compared with the control, suggesting that blood pressure is regulated by ATP2B1 through the contraction and dilation of the vessel, likely by controlling calcium concentrations in the resting state. CONCLUSION: These results support that ATP2B1 is the causative gene in the blood pressure-associated 12q21 locus and demonstrate that ATP2B1 expression in the vessel influences blood pressure.