Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.

Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish.

Isolation and proteomic study of fish liver lipid droplets.

Lipid droplets (LDs) are a neutral lipid storage organelle that is conserved in almost all species. Excessive storage of neutral lipids in LDs is directly associated with many metabolic syndromes. Zebrafish is a better model animal for the study of LD biology due to its transparent embryonic stage compared to other organisms.

Laser-Ironing Induced Capping Layer on Co-ZIF-L Promoting In Situ Surface Modification to High-Spin Oxide-Carbon Hybrids on the "Real Catalyst" for High OER Activity and Stability.

Enhancing electrocatalytic performance through structural and compositional engineering attracts considerable attention. However, most materials only function as pre-catalysts and convert into "real catalysts" during electrochemical reactions. Such transition involves dramatic structural and compositional changes and disrupts their designed properties.

Meloidogyne enterolobii MeMSP1 effector targets the glutathione-S-transferase phi GSTF family in Arabidopsis to manipulate host metabolism and promote nematode parasitism.

Meloidogyne enterolobii is an emerging root-knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M.

The root-knot nematode effector Mi2G02 hijacks a host plant trihelix transcription factor to promote nematode parasitism.

Root-knot nematodes (RKNs) cause huge agricultural losses every year. They secrete a repertoire of effectors to facilitate parasitism through the induction of plant-derived giant feeding cells, which serve as their sole source of nutrients. However, the mode of action of these effectors and their targeted host proteins remain largely unknown.

: Current Implications in Cardiovascular Diseases and Cancers.

Castor zinc finger 1 (CASZ1) is a C2H2 zinc finger family protein that has two splicing variants, CASZ1a and CASZ1b. It is involved in multiple physiological processes, such as tissue differentiation and aldosterone antagonism. Genetic and epigenetic alternations of have been characterized in multiple cardiovascular disorders, such as congenital heart diseases, chronic venous diseases, and hypertension.

Cpeb1b-mediated cytoplasmic polyadenylation of mRNA modulates zebrafish definitive hematopoiesis.

During vertebrate embryogenesis, hematopoietic stem and progenitor cell (HSPC) production through endothelial-to-hematopoietic transition requires suitable developmental signals, but how these signals are accurately regulated remains incompletely understood. Cytoplasmic polyadenylation, which is one of the posttranscriptional regulations, plays a crucial role in RNA metabolism. Here, we report that Cpeb1b-mediated cytoplasmic polyadenylation is important for HSPC specification by translational control of Hedgehog (Hh) signaling during zebrafish early development.

Phase separation of Ddx3xb helicase regulates maternal-to-zygotic transition in zebrafish.

Vertebrate embryogenesis involves a conserved and fundamental process, called the maternal-to-zygotic transition (MZT), which marks the switch from a maternal factors-dominated state to a zygotic factors-driven state. Yet the precise mechanism underlying MZT remains largely unknown. Here we report that the RNA helicase Ddx3xb in zebrafish undergoes liquid-liquid phase separation (LLPS) via its N-terminal intrinsically disordered region (IDR), and an increase in ATP content promotes the condensation of Ddx3xb during MZT.

Organic Fertilization Assembles Fungal Communities of Wheat Rhizosphere Soil and Suppresses the Population Growth of in the Field.

(cereal cyst nematode, CCN) infects wheat and other cereal crops and causes severe losses in their yield. Research has shown that CCN infestations can be mitigated by organic fertilization in wheat fields, but the mechanisms underlying this phenomenon are still largely unknown. In this study, the relationships among CCN, soil properties, and soil fungal communities with organic fertilizer (OF) or chemical fertilizer (CF) and without fertilizer (CK), were investigated for two years in a wheat field in Henan province, China.

Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.

Nascent hematopoietic stem and progenitor cells (HSPCs) acquire definitive hematopoietic characteristics only when they develop into fetal HSPCs; however, the mechanisms underlying fetal HSPC development are poorly understood. Here, we profiled the chromatin accessibility and transcriptional features of zebrafish nascent and fetal HSPCs using ATAC-seq and RNA-seq and revealed dynamic changes during HSPC transition. Functional assays demonstrated that chromatin remodeler-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.

The root-knot nematode effector MiPDI1 targets a stress-associated protein (SAP) to establish disease in Solanaceae and Arabidopsis.

Large amounts of effectors are secreted by the oesophageal glands of plant-parasitic nematodes, but their molecular mode of action remains largely unknown. We characterized a Meloidogyne incognita protein disulphide isomerase (PDI)-like effector protein (MiPDI1) that facilitates nematode parasitism. In situ hybridization showed that MiPDI1 was expressed specifically in the subventral glands of M.

MiMIF-2 Effector of Exhibited Enzyme Activities and Potential Roles in Plant Salicylic Acid Synthesis.

Plant-parasitic nematodes secrete a series of effectors to promote parasitism by modulating host immunity, but the detailed molecular mechanism is ambiguous. Animal parasites secrete macrophage migration inhibitory factor (MIF)-like proteins for evasion of host immune systems, in which their biochemical activities play essential roles. Previous research demonstrated that MiMIF-2 effector was secreted by and modulated host immunity by interacting with annexins.

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function.

Background: Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined.

Results: Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis.

Rab5c-mediated endocytic trafficking regulates hematopoietic stem and progenitor cell development via Notch and AKT signaling.

It is well known that various developmental signals play diverse roles in hematopoietic stem and progenitor cell (HSPC) production; however, how these signaling pathways are orchestrated remains incompletely understood. Here, we report that Rab5c is essential for HSPC specification by endocytic trafficking of Notch and AKT signaling in zebrafish embryos. Rab5c deficiency leads to defects in HSPC production.

The effect of combined application of Streptomyces rubrogriseus HDZ-9-47 with soil biofumigation on soil microbial and nematode communities.

Meloidogyne incognita causes significant damage to many different crops. Previous studies showed that Streptomyces rubrogriseus HDZ-9-47 is a promising biocontrol agent. Combining it with biofumigation improved its efficacy against M.

GLAND5 Effector Interacts With Pyruvate Dehydrogenase Subunit of Plant to Promote Nematode Parasitism.

mainly infects cereal crops and causes severe economic losses. Many studies have shown that parasitic nematodes can secrete effector proteins to suppress plant immune responses and then promote parasitism. In this study, we showed that HaGland5, a novel effector of , was exclusively expressed in dorsal esophageal gland cell of nematode, and up-regulated in the early parasitic stage.

A Novel G16B09-Like Effector From Suppresses Plant Defenses and Promotes Parasitism.

Plant parasitic nematodes secrete effectors into host plant tissues to facilitate parasitism. In this study, we identified a G16B09-like effector protein family from the transcriptome of , and then verified that most of the members could suppress programmed cell death triggered by BAX in . Ha18764, the most homologous to G16B09, was further characterized for its function.

Isolation and characterization of Aspergillus niger NBC001 underlying suppression against Heterodera glycines.

Heterodera glycines is the most pervasive soybean pests worldwide. Biocontrol provides a strategy to sustainably control nematodes. In this study, 22 fungal isolates were obtained and identified from cysts of Heterodera spp.

Two venom allergen-like proteins, HaVAP1 and HaVAP2, are involved in the parasitism of Heterodera avenae.

Despite the fact that venom allergen-like proteins (VAPs) have been identified in many animal- and plant-parasitic nematodes, studies on VAPs in Heterodera avenae, which is an important phytonematode, are still in their infancy. Here, we isolated, cloned and characterized two VAPs, named HaVAP1 and HaVAP2, from H. avenae.

mA modulates haematopoietic stem and progenitor cell specification.

N-methyladenosine (mA) has been identified as the most abundant modification on eukaryote messenger RNA (mRNA). Although the rapid development of high-throughput sequencing technologies has enabled insight into the biological functions of mA modification, the function of mA during vertebrate embryogenesis remains poorly understood. Here we show that mA determines cell fate during the endothelial-to-haematopoietic transition (EHT) to specify the earliest haematopoietic stem/progenitor cells (HSPCs) during zebrafish embryogenesis.

Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of .

Background: The cereal cyst nematode (CCN, ) is a devastating pathogen of wheat and barley crops in many countries. We aimed to prioritize genetic and molecular targets for control via the powerful and integrative bioinformatics platform.

Results: Here, we sequenced mRNA isolated from Chinese at pre-parasitic (consisting of egg, J1 and hatched-J2) stages and post-parasitic (consisting of parasitic-J2, J3, J4 and adults) stages.