Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis Exocyst Subcomplex Containing Subunit EXO70B1 Is Involved in Autophagy‐Related Transport to the Vacuole

Autophagic transport to the vacuole represents an endomembrane trafficking route, which is widely used in plants, not only during stress situations, but also for vacuole biogenesis and during developmental processes. Here we report a role in autophagic membrane transport for EXO70B1—one of 23 paralogs of Arabidopsis EXO70 exocyst subunits. EXO70B1 positive compartments are internalized into the central vacuole and co‐localize with autophagosomal marker ATG8f. This internalization is boosted by induction of autophagy. Loss of function (LOF) mutations in exo70B1 cause reduction of internalized autopagic bodies in the vacuole. Mutant plants also show ectopic hypersensitive response (HR) mediated by salicylic acid (SA) accumulation, increased nitrogen starvation susceptibility and anthocyanin accumulation defects. Anthocyanin accumulation defect persists in npr1x exo70B1 double mutants with SA signaling compromised, while ectopic HR is suppressed. EXO70B1 interacts with SEC5 and EXO84 and forms an exocyst subcomplex involved in autophagy‐related, Golgi‐independent membrane traffic to the vacuole. We show that EXO70B1 is functionally completely different from EXO70A1 exocyst subunit and adopted a specific role in autophagic transport.
A Functional Component of the Transcriptionally Active Chromosome Complex, Arabidopsis pTAC14, Interacts with pTAC12/HEMERA and Regulates Plastid Gene Expression1[W][OA]

The SET domain-containing protein, pTAC14, was previously identified as a component of the transcriptionally active chromosome (TAC) complexes. Here, we investigated the function of pTAC14 in the regulation of plastid-encoded bacterial-type RNA polymerase (PEP) activity and chloroplast development. The knockout of pTAC14 led to the blockage of thylakoid formation in Arabidopsis (Arabidopsis thaliana), and ptac14 was seedling lethal. Sequence and transcriptional analysis showed that pTAC14 encodes a specific protein in plants that is located in the chloroplast associated with the thylakoid and that its expression depends on light. In addition, the transcript levels of all investigated PEP-dependent genes were clearly reduced in the ptac14-1 mutants, while the accumulation of nucleus-encoded phage-type RNA polymerase-dependent transcripts was increased, indicating an important role of pTAC14 in maintaining PEP activity. pTAC14 was found to interact with pTAC12/HEMERA, another component of TACs that is involved in phytochrome signaling. The data suggest that pTAC14 is essential for proper chloroplast development, most likely by affecting PEP activity and regulating PEP-dependent plastid gene transcription in Arabidopsis together with pTAC12.
Prognostic value of quantitative immune alterations in melanoma patients

• Purpose: The immune response is altered in patients with neoplasms. Immunosuppression has important consequences in patients with melanoma. The aim of this study was to assess quantitative immune alterations in melanoma patients. • Material and methods: We obtained a peripheral blood sample in EDTA from 86 melanoma patients (63 of them disease-free and 23 with distant disease). Total leukocytes and lymphocytes, B lymphocytes (CD19), types CD3, CD4, CD8 lymphocytes, and NK lymphocytes (CD56) were counted by determining the surface markers by flow cytometry, using a Coulter Epics Elite (Coulter Corp.). IgA, IgG, IgE and IgM were assayed by nephelometric methods employing a Hyland PDQ laser nephelometer. • Results: We found significant differences between disease-free patients and those with active disease with regard to lymphocytes total count (median: 2251.57 vs. 1783.04/mm 3 , p=0.010), NK lymphocytes (CD56) (149.54 vs. 115.2/mm 3 , p=0.016), and IgA levels (241.59 vs. 300.55 mg/dl, p=0.044), when taken as continuous variables. When considering each parameter as a discontinuous variable, only changes in absolute lymphocyte count retained an statistical difference depending on the presence or absence of active disease, 73.9% of the patients with active metastatic disease having a lymphocyte count below 2000 cells/mm 3 versus only 36.5% of the disease-free patients (c2 Pearson=9.476, df=1, p=0.002). The median survival for the 46 patients with absolute lymphocyte count above 2000 cells/mm 3 was 965 days (DF=65.03, IC 95%=792.72-1090.30) versus 441 days (DF=75.61, IC 95%=292.81-589.19) for the 40 patients with absolute lymphocyte count below 2000 cells/mm3 (log rank=4.54, df=1, p=0.0331). • Conclusions: There are significant differences in some lymphocyte populations and IgA levels between patients with metastases and disease-free patients. Melanoma patients with absolute lymphocyte levels above 2000 cells/mm3 have a longer survival than those with a lymphocyte count below 2000 cells/mm 3 .
LYST Affects Lysosome Size and Quantity, but not Trafficking or Degradation Through Autophagy or Endocytosis

Mutations in the large BEACH domain‐containing protein LYST causes Chediak–Higashi syndrome. The diagnostic hallmark is enlarged lysosomes and lysosome‐related organelles in various cell types. Dysfunctional secretion of enlarged lysosome‐related organelles has been observed in cells with mutations in LYST, but the capacity of the enlarged lysosomes to degrade endogenous proteins has not been studied. Here, we show for the first time that small interfering RNA‐depletion of LYST in human cell lines recapitulates the LYST mutant phenotype of enlarged lysosomes. We found no evidence for an effect of LYST depletion on autophagy or endocytic degradation. Autophagosomes are formed in normal size and quantities and are able to fuse to the enlarged lysosomes, leading to normal rates of degradation. Degradation of the epidermal growth factor receptor (EGFR) was similarly not affected, indicating that the enlarged lysosomes are fully functional in degrading endogenous proteins. Retrograde trafficking of toxins as well as the localization of transporters of lysosomal proteins, adaptor protein‐3 (AP‐3) and cation‐independent mannose‐6‐phosphate receptor (CI‐MPR), were all found to be unaffected by LYST. Quantitative analysis of the enlarged lysosomes shows that LYST depletion causes a reduction in vesicle quantity per cell, while the total enzymatic content and vesicular pH are unaffected, supporting a role for LYST in lysosomal fission and/or fusion events.
Phenothiazine‐Derived Antipsychotic Drugs Inhibit Dynamin and Clathrin‐Mediated Endocytosis

Chlorpromazine is a phenothiazine‐derived antipsychotic drug (APD) that inhibits clathrin‐mediated endocytosis (CME) in cells by an unknown mechanism. We examined whether its action and that of other APDs might be mediated by the GTPase activity of dynamin. Eight of eight phenothiazine‐derived APDs inhibited dynamin I (dynI) in the 2–12 µm range, the most potent being trifluoperazine (IC50 2.6 ± 0.7 µm). They also inhibited dynamin II (dynII) at similar concentrations. Typical and atypical APDs not based on the phenothiazine scaffold were 8‐ to 10‐fold less potent (haloperidol and clozapine) or were inactive (droperidol, olanzapine and risperidone). Kinetic analysis showed that phenothiazine‐derived APDs were lipid competitive, while haloperidol was uncompetitive with lipid. Accordingly, phenothiazine‐derived APDs inhibited dynI GTPase activity stimulated by lipids but not by various SH3 domains. All dynamin‐active APDs also inhibited transferrin (Tfn) CME in cells at related potencies. Structure–activity relationships (SAR) revealed dynamin inhibition to be conferred by a substituent group containing a terminal tertiary amino group at the N2 position. Chlorpromazine was previously proposed to target AP‐2 recruitment in the formation of clathrin‐coated vesicles (CCV). However, neither chlorpromazine nor thioridazine affected AP‐2 interaction with amphiphysin or clathrin. Super‐resolution microscopy revealed that chlorpromazine blocks neither clathrin recruitment by AP‐2, nor AP‐2 recruitment, showing that CME inhibition occurs downstream of CCV formation. Overall, potent dynamin inhibition is a shared characteristic of phenothiazine‐derived APDs, but not other typical or atypical APDs, and the data indicate that dynamin is their likely in‐cell target in endocytosis.
Regulatory Functions of SnRK1 in Stress-Responsive Gene Expression and in Plant Growth and Development1[C][W][OA]

Sucrose-nonfermentation1-related protein kinase1 (SnRK1) is an evolutionarily conserved energy sensor protein that regulates gene expression in response to energy depletion in plants. Efforts to elucidate the functions and mechanisms of this protein kinase are hampered, however, by inherent growth defects of snrk1-null mutant plants. To overcome these limitations and study SnRK1 functions in vivo, we applied a method combining transient expression in leaf mesophyll protoplasts and stable expression in transgenic plants. We found that both rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) SnRK1 activities critically influence stress-inducible gene expression and the induction of stress tolerance. Genetic, molecular, and chromatin immunoprecipitation analyses further revealed that the nuclear SnRK1 modulated target gene transcription in a submergence-dependent manner. From early seedling development through late senescence, SnRK1 activities appeared to modulate developmental processes in the plants. Our findings offer insight into the regulatory functions of plant SnRK1 in stress-responsive gene regulation and in plant growth and development throughout the life cycle.
The Crossroads of Synaptic Growth Signaling, Membrane Traffic and Neurological Disease: Insights from Drosophila

Neurons require target‐derived autocrine and paracrine growth factors to maintain proper identity, innervation, homeostasis and survival. Neuronal growth factor signaling is highly dependent on membrane traffic, both for the packaging and release of the growth factors themselves, and for regulation of intracellular signaling by their transmembrane receptors. Here, we review recent findings from the Drosophila larval neuromuscular junction (NMJ) that illustrate how specific steps of intracellular traffic and inter‐organelle interactions impinge on signaling, particularly in the bone morphogenic protein, Wingless and c‐Jun‐activated kinase pathways, regulating elaboration and stability of NMJ arbors, construction of synapses and synaptic transmission and homeostasis. These membrane trafficking and signaling pathways have been implicated in human motor neuron diseases including amyotrophic lateral sclerosis and hereditary spastic paraplegia, highlighting their importance for neuronal health and survival.
Reactive Oxygen Species-Driven Transcription in Arabidopsis under Oxygen Deprivation1[W]

Reactive oxygen species (ROS) play an important role as triggers of gene expression during biotic and abiotic stresses, among which is low oxygen (O2). Previous studies have shown that ROS regulation under low O2 is driven by a RHO-like GTPase that allows tight control of hydrogen peroxide (H2O2) production. H2O2 is thought to regulate the expression of heat shock proteins, in a mechanism that is common to both O2 deprivation and to heat stress. In this work, we used publicly available Arabidopsis (Arabidopsis thaliana) microarray datasets related to ROS and O2 deprivation to define transcriptome convergence pattern. Our results show that although Arabidopsis response to anoxic and hypoxic treatments share a common core of genes related to the anaerobic metabolism, they differ in terms of ROS-related gene response. We propose that H2O2 production under O2 deprivation is a trait present in a very early phase of anoxia, and that ROS are needed for the regulation of a set of genes belonging to the heat shock protein and ROS-mediated groups. This mechanism, likely not regulated via the N-end rule pathway for O2 sensing, is probably mediated by a NADPH oxidase and it is involved in plant tolerance to the stress.
A Caenorhabditis elegans Homologue of LYST Functions in Endosome and Lysosome‐Related Organelle Biogenesis

While the trafficking pathways that mediate the delivery of proteins to lysosome‐related organelles (LROs) are becoming increasingly clear, how LRO size and numbers are controlled is relatively unstudied. BEACH domain containing proteins (BDCPs) have emerged as potential regulators of these processes. Caenorhabditis elegans lyst‐1 encodes a BDCP that is homologous to both human LYST, which is mutated in Chediak‐Higashi syndrome, and NBEAL2, which is mutated in gray platelet syndrome. We show that mutations in lyst‐1 lead to fragmentation of intestinal specific LROs called gut granules. Protein trafficking to gut granules appears to be unaffected in lyst‐1(−) mutants; however, gut granule formation and function is disrupted. We find that lysosomes are smaller in both intestinal cells and coelomocytes of lyst‐1(−) mutants. We show that mutations in the three other BDCPs encoded by C. elegans do not similarly alter gut granule morphology. While recycling and late endosomes appear to be unaltered, mutations in lyst‐1 cause a significant reduction in the number of RAB‐5::GFP containing early endosomes, an effect that has not been reported for any other BDCP mutant.
Reactive Oxygen Species Are Involved in Gibberellin/Abscisic Acid Signaling in Barley Aleurone Cells1[C][W][OA]

Reactive oxygen species (ROS) act as signal molecules for a variety of processes in plants. However, many questions about the roles of ROS in plants remain to be clarified. Here, we report the role of ROS in gibberellin (GA) and abscisic acid (ABA) signaling in barley (Hordeum vulgare) aleurone cells. The production of hydrogen peroxide (H2O2), a type of ROS, was induced by GA in aleurone cells but suppressed by ABA. Furthermore, exogenous H2O2 appeared to promote the induction of α-amylases by GA. In contrast, antioxidants suppressed the induction of α-amylases. Therefore, H2O2 seems to function in GA and ABA signaling, and in regulation of α-amylase production, in aleurone cells. To identify the target of H2O2 in GA and ABA signaling, we analyzed the interrelationships between H2O2 and DELLA proteins Slender1 (SLN1), GA-regulated Myb transcription factor (GAmyb), and ABA-responsive protein kinase (PKABA) and their roles in GA and ABA signaling in aleurone cells. In the presence of GA, exogenous H2O2 had little effect on the degradation of SLN1, the primary transcriptional repressor mediating GA signaling, but it promoted the production of the mRNA encoding GAMyb, which acts downstream of SLN1 and involves induction of α-amylase mRNA. Additionally, H2O2 suppressed the production of PKABA mRNA, which is induced by ABA:PKABA represses the production of GAMyb mRNA. From these observations, we concluded that H2O2 released the repression of GAMyb mRNA by PKABA and consequently promoted the production of α-amylase mRNA, thus suggesting that the H2O2 generated by GA in aleurone cells is a signal molecule that antagonizes ABA signaling.
Principles of Virus Uncoating: Cues and the Snooker Ball

Viruses are spherical or complex shaped carriers of proteins, nucleic acids and sometimes lipids and sugars. They are metastable and poised for structural changes. These features allow viruses to communicate with host cells during entry, and to release the viral genome, a process known as uncoating. Studies have shown that hundreds of host factors directly or indirectly support this process. The cell provides molecules that promote stepwise virus uncoating, and direct the virus to the site of replication. It acts akin to a snooker player who delivers accurate and timely shots (cues) to the ball (virus) to score. The viruses, on the other hand, trick (snooker) the host, hijack its homeostasis systems, and dampen innate immune responses directed against danger signals. In this review, we discuss how cellular cues, facilitators, and built‐in viral mechanisms promote uncoating. Cues come from receptors, enzymes and chemicals that act directly on the virus particle to alter its structure, trafficking and infectivity. Facilitators are defined as host factors that are involved in processes which indirectly enhance entry or uncoating. Unraveling the mechanisms of virus uncoating will continue to enhance understanding of cell functions, and help counteracting infections with chemicals and vaccines.
Surviving childhood cancer: A descriptive approach to understanding the impact of life‐threatening illness

Descriptive findings are presented from a study of adult survivors of childhood cancer. Most survivors reported having coped well with illness. When asked about various life domains, in all cases a majority saw cancer experience as having had a positive impact over the long term. Despite the overall good adaptation of survivors, illness experience was traumatic at the time and it continued to cause difficulties. School, work and physical symptoms caused problems for a proportion of survivors—with greater representation from among those treated for brain tumours. One‐quarter of survivors felt that they currently had insufficient medical information. Interpersonal relationships, although greatly valued and heavily invested in by survivors, were also frequently characterized by heightened sensitivity and cautiousness. Finally, a small minority of cancer survivors showed considerable adjustment difficulties, most notably in the area of social relations. Descriptive findings are integrated with findings from comparisons of survivors to a group of healthy peers. Implications of study findings for research directions and program development are discussed.
Congenital pancreatoblastoma associated with β‐catenin mutation

To the Editor: Pancreatoblstoma (PB) is a rare primary neoplasm of childhood. Although 200 cases of PB have been reported, it is considered the most common neoplasm in early childhood pancreatic tumors [1]. Most PB cases are sporadic and the congenital cases of PB have been described in association with Beckwith–Wiedemann syndrome (BWS) [2]. PB molecular pathogenesis remains to be elucidated. Genetic alterations of the adenomatous polyposis coli (APC)/b-catenin pathway and chromosome 11p loss of heterozygosity (LOH) are the most frequent molecular events in PB [3]. In pediatric neoplasms, ß-catenin mutation frequently found in hepatoblastoma [4] and pancreatoblastoma [3]. Here, we report a case of PB presenting in a 3-day-old male without any other congenital anomalies. On examination, there was an intra-abdominal mass that was confirmed by radiographic examination. Laboratory findings included elevated serum levels for a-fetoprotein of 272,680 ng/ml and lactate dehydrogenase of 518 IU/L. Complete resection of the tumor was performed and the patient recovered after surgery without complications. HEstained sections of the resected tumor, showed the typical histopathology of PB. Immumohistochemistry showed nuclear and cytoplasmic accumulation of b-catenin (CTNB1) and cyclin D1 proteins in PB specimen. We found a novel point mutation in codon 41 (A to G) resulting in a substitution of threonine by alanine in PB tissue from which gDNA was available. A crucial effector of Wnt signaling is b-catenin, a multifunctional protein that plays important roles in intercellular adhesion and in cell growth, survival, and differentiation [5]. Koesters and von Knebel Doeberitz [6] demonstrated that mutations in codon 41/45 of b-catenin had a higher oncogenic potential than mutations affecting the codon 33/37 cluster region in rat colon tumors induced by the alkylating agent. Our report shows the isolated congenital form of PB with point mutation in codon 41 of bcatenin gene. This study supports the notion that Wnt signaling pathway plays an important role in tumorgenesis of PB. Full benefit from early diagnosis of this rare entity of neoplasm will enable us to learn more of its biology.
The High-Affinity Phosphate Transporter GmPT5 Regulates Phosphate Transport to Nodules and Nodulation in Soybean1[W][OA]

Legume biological nitrogen (N) fixation is the most important N source in agroecosystems, but it is also a process requiring a considerable amount of phosphorus (P). Therefore, developing legume varieties with effective N2 fixation under P-limited conditions could have profound significance for improving agricultural sustainability. We show here that inoculation with effective rhizobial strains enhanced soybean (Glycine max) N2 fixation and P nutrition in the field as well as in hydroponics. Furthermore, we identified and characterized a nodule high-affinity phosphate (Pi) transporter gene, GmPT5, whose expression was elevated in response to low P. Yeast heterologous expression verified that GmPT5 was indeed a high-affinity Pi transporter. Localization of GmPT5 expression based on β-glucuronidase staining in soybean composite plants with transgenic roots and nodules showed that GmPT5 expression occurred principally in the junction area between roots and young nodules and in the nodule vascular bundles for juvenile and mature nodules, implying that GmPT5 might function in transporting Pi from the root vascular system into nodules. Overexpression or knockdown of GmPT5 in transgenic composite soybean plants altered nodulation and plant growth performance, which was partially dependent on P supply. Through both in situ and in vitro 33P uptake assays using transgenic soybean roots and nodules, we demonstrated that GmPT5 mainly functions in transporting Pi from roots to nodules, especially under P-limited conditions. We conclude that the high-affinity Pi transporter, GmPT5, controls Pi entry from roots to nodules, is critical for maintaining Pi homeostasis in nodules, and subsequently regulates soybean nodulation and growth performance.
The management of menstrual suppression and uterine bleeding: A survey of current practices in the pediatric blood and marrow transplant consortium

Current guidelines recommend the use of combined hormonal contraceptive pills for menstrual suppression in pediatric blood and marrow transplant (BMT) recipients but recent research reveals that provider practice varies. This study was designed to describe the current practice for managing menstrual issues, that is, menstrual suppression and uterine bleeding, in pediatric BMT patients and to better understand health care providers' practices in the use of gonadotropin‐releasing hormone agonists (GnRHa).
Barley Stripe Mosaic Virus-Mediated Tools for Investigating Gene Function in Cereal Plants and Their Pathogens: Virus-Induced Gene Silencing, Host-Mediated Gene Silencing, and Virus-Mediated Overexpression of Heterologous Protein1

Barley stripe mosaic virus ([BSMV][1]), the Hordeivirus type member, is the most intensely studied virus that naturally infects two major monocot crops, wheat ( Triticum aestivum ) and barley ( Hordeum vulgare ). The tripartite genome of this virus, comprising RNAα, RNAβ, and RNAγ, was sequenced