Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant-growth promoting effect of newly isolated rhizobacteria varies between two Arabidopsis ecotypes

Various rhizobacteria are known for their beneficial effects on plants, i. e. promotion of growth and induction of systemic resistance against pathogens. These bacteria are categorized as plant growth promoting rhizobacteria (PGPR) and are associated with plant roots. Knowledge of the underlying mechanisms of plant growth promotion in vivo is still very limited, but interference of bacteria with plant hormone metabolism is suggested to play a major role. To obtain new growth promoting bacteria, we started a quest for rhizobacteria that are naturally associated to Arabidopsis thaliana. A suite of native root-associated bacteria were isolated from surface-sterilized roots of the Arabidopsis ecotype Gol-1 derived from a field site near Golm (Berlin area, Germany). We found several Pseudomonas and a Microbacterium species and tested these for growth promotion effects on the Arabidopsis ecotypes Gol-1 and Col-0, and for growth-promotion associated traits, such as auxin production, ACC deaminase activity and phosphate solubilization capacity. We showed that two of the bacteria strains promote plant growth with respect to rosette diameter, stalk length and accelerate development and that the effects were greater when bacteria were applied to Col-0 compared with Gol-1. Furthermore, the capability of promoting growth was not explained by the tested metabolic properties of the bacteria, suggesting that further bacterial traits are required. The natural variation of growth effects, combined with the extensive transgenic approaches available for the model plant Arabidopsis, will build a valuable tool to augment our understanding of the molecular mechanisms involved in the natural Arabidopsis - PGPR association.
No evidence for the occurrence of substrate inhibition of Arabidopsis thaliana sucrose synthase-1 (AtSUS1) by fructose and UDP-glucose

Sucrose synthase (SuSy) catalyzes the reversible conversion of sucrose and NDP into the corresponding nucleotide-sugars and fructose. The Arabidopsis genome possesses six SUS genes (AtSUS1–6) that code for proteins with SuSy activity. As a first step to investigate optimum fructose and UDP-glucose (UDPG) concentrations necessary to measure maximum sucrose-producing SuSy activity in crude extracts of Arabidopsis, in this work we performed kinetic analyses of recombinant AtSUS1 in two steps: (1) SuSy reaction at pH 7.5, and (2) chromatographic measurement of sucrose produced in step 1. These analyses revealed a typical Michaelis-Menten behavior with respect to both UDPG and fructose, with Km values of 50 μM and 25 mM, respectively. Unlike earlier studies showing the occurrence of substrate inhibition of UDP-producing AtSUS1 by fructose and UDP-glucose, these analyses also revealed no substrate inhibition of AtSUS1 at any UDPG and fructose concentration. By including 200 mM fructose and 1 mM UDPG in the SuSy reaction assay mixture, we found that sucrose-producing SuSy activity in leaves and stems of Arabidopsis were exceedingly higher than previously reported activities. Furthermore, we found that SuSy activities in organs of the sus1/sus2/sus3/sus4 mutant were ca. 80–90% of those found in WT plants.
The unliganded long isoform of estrogen receptor beta stimulates brain ryanodine receptor single channel activity alongside with cytosolic Ca2+

Ca2+ release from intracellular stores mediated by endoplasmic reticulum membrane ryanodine receptors (RyR) plays a key role in activating and synchronizing downstream Ca2+-dependent mechanisms, in different cells varying from apoptosis to nuclear transcription and development of defensive responses. Recently discovered, atypical “nongenomic” effects mediated by estrogen receptors (ER) include rapid Ca2+ release upon estrogen exposure in conditions implicitly suggesting involvement of RyRs. In the present study, we report various levels of colocalization between RyR type 2 (RyR2) and ER type β (ERβ) in the neuronal cell line HT-22, indicating a possible functional interaction. Electrophysiological analyses revealed a significant increase in single-channel ionic currents generated by mouse brain RyRs after application of the soluble monomer of the long form ERβ (ERβ 1). The effect was due to a strong increase in open probability of RyR higher open channel sublevels at cytosolic [Ca2+] concentrations of 100 nM, suggesting a synergistic action of ERβ1 and Ca2+ in RyR activation, and a potential contribution to Ca2+-induced Ca2+ release rather than to basal intracellular Ca2+ concentration level at rest. This RyR/ERβ interaction has potential effects on cellular physiology, including roles of shorter ERβ isoforms and modulation of the RyR/ERβ complexes by exogenous estrogens.
The estrogen-related receptor alpha: the oldest, yet an energetic orphan with robust biological functions

The estrogen-related receptor alpha (ERRα) is an orphan nuclear receptor (ONR) that by binding to DNA sites controls gene expression in association with coactivators and corepressors. ERRα was the first ONR to be identified; however, its natural endogenous ligand(s) is still unknown. ERRα by acting as a transcription factor has been shown to regulate a large array of genes, thereby controlling numerous metabolic pathways and other biological functions in animals. Of late, the expression of ERRα has been detected in several tissues, including those with high metabolic activities and energy demand. Presently, the control of energy balance by ERRα seems to be its prime role. The nonavailability of endogenous ligand for ERRα has not impeded the study of its functions. In fact, most of the present knowledge of the biological roles of ERRα has evolved from in-depth biochemical, overexpression, genomic, including functional genomics studies, and also through the generation of intact ERRα knockout (null) mice. Interestingly, over the past few years, growing evidence suggests interplay between ERRα and various human metabolic diseases such as diabetes, obesity, and heart disease. Also, there are strong indications of the involvement of ERRα in cancer initiation and progression. Interestingly, this makes ERRα a suitable, direct target for pharmacological intervention in treating such diseases. This review focuses on the overall developments and recent advances in understanding the role of ERRα in metabolism and other biological functions, including its role in human diseases.
Novel features of radiation-induced bystander signaling in Arabidopsis thaliana demonstrated using root micro-grafting

Radiation-induced bystander effects (RIBE) have been well demonstrated in whole organisms, as well as in single-cell culture models in vitro and multi-cellular tissues models in vitro, however, the underlying mechanisms remain unclear, including the temporal and spatial course of bystander signaling. The RIBE in vivo has been shown to exist in the model plant Arabidopsis thaliana (A. thaliana). Importantly, the unique plant grafting provides a delicate approach for studying the temporal and spatial course of bystander signaling in the context of whole plants. In our previous study, the time course of bystander signaling in plants has been well demonstrated using the root micro-grafting technique. In this study, we further investigated the temporal cooperation pattern of multiple bystander signals, the directionality of bystander signaling, and the effect of bystander tissues on the bystander signaling. The results showed that the bystander response could also be induced efficiently when the asynchronously generated bystander signals reached the bystander tissues in the same period, but not when they entered into the bystander tissues in an inversed sequence. The absence of bystander response in root-inversed grafting indicated that the bystander signaling along roots might be of directionality. The bystander signaling was shown to be independent of the bystander tissues.
Abundance of mixed linkage glucan in mature tissues and secondary cell walls of grasses

(1,3; 1,4)-β-D-glucan, also known as mixed linkage glucan (MLG), is a polysaccharide that in flowering plants is unique to the cell walls of grasses and other related members of Poales. MLG is highly abundant in endosperm cell walls, where it is considered a storage carbohydrate. In vegetative tissues, MLG transiently accumulates in the primary cell walls of young, elongating organs. In evolutionary distant species such as Equisetum, MLG accumulates predominantly in old tissues in the stems. Similarly, we have recently shown that rice accumulates a large amount of MLG in mature stems, which prompted us to re-evaluate the hypothesis that MLG is solely related to growth in grass vegetative tissues. Here, we summarize data that confirms the presence of MLG in secondary cell walls and mature tissues in rice and other grasses. Along with these results, we discuss additional evidence indicating a broader role for MLG than previously considered.
Cis- and trans-zeatin differentially modulate plant immunity

Phytohormones are essential regulators of various processes in plant growth and development. Several phytohormones are also known to regulate plant responses to environmental stress and pathogens. Only recently, cytokinins have been demonstrated to play an important role in plant immunity. Increased levels of cytokinins such as trans-zeatin, which are considered highly active, induced resistance against mainly (hemi)biotrophic pathogens in different plant species. In contrast, cis-zeatin is commonly regarded as a cytokinin exhibiting low or no activity. Here we comparatively study the impact of both zeatin isomers on the infection of Nicotiana tabacum by the (hemi)biotrophic microbial pathogen Pseudomonas syringae. We demonstrate a biological effect of cis-zeatin and a differential effect of the two zeatin isomers on symptom development, defense responses and bacterial multiplication.
Identification of phasiRNAs in wild rice (Oryza rufipogon)

Plant miRNAs can trigger the production of phased, secondary siRNAs from either non-coding or protein-coding genes. In this study, at least 864 and 3,961 loci generating 21-nt and 24-nt phased siRNAs (phasiRNAs),respectively, were identified in three tissues from wild rice. Of these phasiRNA-producing loci, or PHAS genes, biogenesis of phasiRNAs in at least 160 of 21-nt and 254 of 24-nt loci could be triggered by interaction with miRNA(s). Developing seeds had more PHAS genes than leaves and roots. Genetic constrain on miRNA-triggered PHAS genes suggests that phasiRNAs might be one of the driving forces contributed to rice domestication.
Pharmacophore modeling, 3D-QSAR and DFT studies of IWR small-molecule inhibitors of Wnt response

Abstract In this study, a 5-point pharmacophore model was developed and the model was used to generate a predictive atom-based 3D quantitative structure activity relationship (3D-QSAR) analysis for the studied dataset of 50 compounds. The obtained 3D-QSAR model shows correlation coefficient (R2) of 0.87 for training set compounds and excellent predictive power (Q2) of 0.81 for cross-validated test set compounds. External validation indicated that our 3D-QSAR model has high predictive power with and values of 0.99 and 0.65, respectively. The most active and least active compounds were further optimized using density functional theory at B3LYP/3-21*G level. Further, pharmacophoric model was employed for pharmacophore-based screening to identify potential inhibitors against Wnt/β-catenin pathway. Hence, these molecules could act as selective inhibitors of Wnt/β-catenin pathway which can be experimentally validated. The backbone of these inhibitors could serve as templates for designing drug-like molecules specifically targeting Wnt/β-catenin pathway.
The MIXTA-like Transcription factor MYB16 is a major regulator of cuticle formation in vegetative organs

Cuticle secreted on the surface of the epidermis of aerial organs protects plants from the external environment. We recently found that Arabidopsis MIXTA-like R2R3-MYB family members MYB16 and MYB106 regulate cuticle formation in reproductive organs and trichomes. However, the artificial miRNA (amiRNA)-mediated knockdown plants showed no clear phenotypic abnormality in vegetative tissues. In this study, we used RNA interference (RNAi) targeting MYB16 to produce plants with reduced expression of both MYB16 and MYB106. The rosette leaves of RNAi plants showed more severe permeable cuticle phenotypes than the myb106 mutants expressing the MYB16 amiRNA in the previous study. The RNAi plants also showed reduced expression of cuticle biosynthesis genes LACERATA and ECERIFERUM1. By contrast, expression of a gain-of-function MYB16 construct induced over-accumulation of waxy substances on leaves. These results suggest that MYB16 functions as a major regulator of cuticle formation in vegetative organs, in addition to its effect in reproductive organs and trichomes.
Allele-specific effects of PDF2 on floral morphology in Arabidopsis thaliana

The class IV Homeodomain-leucine zipper (HD-ZIP IV) gene family includes several genes that are functionally significant in epidermal development. Our recent study revealed that double mutants of the epidermis-expressed HD-ZIP IV members, PROTODERMAL FACTOR2 (PDF2) in combination with some HOMEODOMAIN GLABROUS (HDG, pronounced “hedge”) genes, affect stamen development and specification of petal and stamen identity, possibly in a non cell-autonomous manner. However, the effect of the pdf2 mutations on the floral development was largely different depending on T-DNA insertion locations: pdf2–1 hdg flowers exhibited homeotic conversion of petals and stamens, while pdf2–2 hdg flowers had only a reduced number of stamens. Here, we used 2 additional pdf2 alleles to make double mutants and found that their floral phenotypes were rather similar to those of pdf2–2 hdg. The allele-specific effect caused by pdf2–1, which carries a T-DNA in a steroidogenic acute regulatory protein-related lipid transfer (START) domain-encoding region, suggests the importance of the START domain in proper function of HD-ZIP IV proteins.
Comparison of Functional Walking Training Using Concentric-Eccentric Resistance on Hip Muscle Strength, Balance, and Functional Mobility in Working and Retired Older Adults

Background: Age-related lower extremity weakness leads to difficulty with stair negotiation, gait, and balance. The purpose of this study was to evaluate and compare the impact of functional walking training on hip strength, balance, and functional mobility among community-dwelling working and retired older adults. Methods: 12 healthy working adults (10 females and 2 males; mean age 66 years) were recruited from the campus community and 15 retired community-dwelling adults (13 females and 2 males; mean age 75 years) were recruited from a church. Subjects completed pre-post-test measurements: hip strength (flexion, abduction, and extension) were tested using hand held dynamometer; Timed Up and Go test, 30-Second Chair Rise test, and static and dynamic balance tested using the Zeno Walkway System. Subjects completed 8 sessions of functional walking using the BTE TM Primus RS. Subjects were connected to the Primus using cable attachment and waist belt. Primus was set in concentric-eccentric mode and resistance was applied. Subjects walked seven feet in four directions: forward; backward; sideways both directions a total of five times each. Resistance was increased each session. Results: The working group had significant improvements (p= 0.02-0.0003) in Timed Up and Go, 30-Second Chair Rise test, and hip strength following the intervention. The retired group had significant (p=0.01-0.0002) improvements in Timed Up and Go, 30-Second Chair Rise, hip strength, and dynamic balance. Neither group showed statistically significant changes in static balance. Only the Timed Up and Go was significantly different in the amount of change between groups. Conclusion: A resisted functional walking program resulted in significant improvements in function and strength in both working and retired older adults. Functional walking with resistance allows older adults to benefit without having them assume difficult exercise positions. This exercise protocol can be easily modified for the clinical setting and be used in falls prevention programs.
Arabidopsis CAP1-mediated ammonium sensing required reactive oxygen species in plant cell growth

[Ca2+]cyt-associated protein kinase (CAP) gene 1 is a receptor-like kinase that belongs to CrRLK1L (Catharanthus roseus Receptor like kinase) subfamily. CAP1 has been identified as a novel modulator of NH4+ in the tonoplast, which regulates root hair growth by maintaining the cytoplasmic Ca2+ gradients. Different expression pattern of tonoplast intrinsic protein (TIP2;3) in the CAP1 knock out mutant and wild type on Murashige and Skoog (MS) medium suggested that CAP1 influences transport activity to regulate the compartmentalization of NH4+ into vacuole. Lower expression level of Oxidative Signal-Inducible1(OXI1) in the cap1-1 root and the abnormal reactive oxygen species (ROS) gradient in root hair of cap1-1 on MS medium indicated that ROS signaling involve in CAP1-regulated root hair growth. Wild-type-like ROS distribution pattern in the cap1-1 root hair can be reestablished in seedlings grown on NH4+ deficient medium, which indicated that CAP1 functions as a sensor for NH4+ signaling in maintaining tip-focused ROS gradient in root hairs polar growth.
Eating Disorders and Body Image Perception among University Students

This study aimed to determine the prevalence of eating disorders and body image among university students undertaking nutrition education. Subjects included 577 students from Gazi University, Faculty of Vocational Education, Department of Food and Nutrition Education (Group 1 n = 299) and other departments (Group 2 n = 278) which did not involve nutrition education. The Eating Attitudes Test (EAT-40), body cathexis index and anthropometric measurements were used to assess eating attitudes. The results showed that 75.9% of nutrition educated students and 83.5% of others had normal BMI (18.5-24.9 kg/m ). 2 Thirty-four of the 577 students had an EAT-40 score over the cut-off level of 30. Thus, 14% of the nutrition educated were at high risk and 9.7% at moderate risk. Among others, 7.2% were at high risk and 13.3% at moderate risk. It was also seen that 30.1% of the nutrition educated and 29.5% of others were dissatisfied with their bodies. The mean EAT-40 score of all participants was 15.1±10.68; body cathexis score was 147.9±21.48. The difference between the two index means was not significant (p>0.05). A weak negative relationship was found between BMI, EAT-40 and the body image perception score. The results indicated that the prevalence of abnormal eating attitudes and behaviors was 5.9% among students. Nutrition education was found to have no effect on the occurrence of abnormal eating attitudes and behaviors.
The non-coding RNA world of the bacterial pathogen Listeria monocytogenes

In the past ten years, Listeria monocytogenes has emerged as a model organism in infection biology and also become an attractive system for the study of regulatory RNAs in pathogenic bacteria. Due to the recent completion of several transcriptomic studies, it is now clear that L. monocytogenes possesses a large repertoire of both cis- and trans-encoded RNAs. These include numerous small RNAs (sRNAs) expressed during infection, widespread transcription of both short and long antisense RNAs (asRNAs) and an array of cis-acting regulatory RNA elements. In this review we highlight the recent advances in non-coding RNA research in L. monocytogenes with a particular focus on emerging themes of RNA-based regulation.
A Pilot Training Program for a Motivational Enhancement Approach to Hepatitis C Virus Treatment Among Individuals in Israeli Methadone Treatment Centers

Although hepatitis C virus (HCV) can be cleared, very few infected persons complete the treatment, resulting in disease progression and transmission. Motivational interventions effectively address health and substance-use-related conditions in many cultures. The research team piloted an HCV treatment motivational enhancement training and supervision for four counselors treating four patients in one (of 11) large methadone programs in Israel between 2007 and 2008. The counselors received a 3-day training followed by seven supervision sessions. Training included cultural and language adaptation from the original United States version to practice in Israel. Feasibility was assessed and demonstrated through training field notes and questionnaire feedback, review of taped intervention sessions for counselor proficiency and patient engagement, and patient completion of intervention sessions and piloted measures. While positive feasibility outcomes were noted, future studies should employ larger numbers of counselors and patients to assess the effectiveness of motivational enhancement in promoting HCV treatment in methadone patients.
The Unheard Pain of Cancer Patients

Cancer pain is multidimensional and complex mechanism rarely presenting as a pure neuropathic, visceral, or somatic pain syndrome. Rather, it may involve inflammatory, neuropathic, ischemic, breakthrough pain mechanisms at multiple sites. Despite recommendation and demonstration of patients′ need, these needs are not being met. Since two decades, a trend has been set to exclude pain specialist from mainstream cancer pain management, they are being called during the end stage making them the ′last resort′. Thus patients are missing out on benefits of multidisciplinary care combining palliative care and pain medicine. Morphine licensing is still a very painful procedure for the institutions trying to provide pain relief to the cancer patients and due to this troublesome procedure of morphine licensing many patients do not get adequate analgesia and die in pain. This review article highlights the importance of recognizing cancer-related pain and the need to optimize management. It emphasizes on pain management for the cancer population with evidence-based multimodal and mechanism-based treatments and finally to strengthen the relationship between palliative care, oncology, and pain medicine.
A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes

The pentatricopeptide repeat modules of PPR proteins are key to their sequence-specific binding to RNAs. Gene families encoding PPR proteins are greatly expanded in land plants where hundreds of them participate in RNA maturation, mainly in mitochondria and chloroplasts. Many plant PPR proteins contain additional carboxyterminal domains and have been identified as essential factors for specific events of C-to-U RNA editing, which is abundant in the two endosymbiotic plant organelles. Among those carboxyterminal domain additions to plant PPR proteins, the so-called DYW domain is particularly interesting given its similarity to cytidine deaminases. The frequency of organelle C-to-U RNA editing and the diversity of DYW-type PPR proteins correlate well in plants and both were recently identified outside of land plants, in the protist Naegleria gruberi. Here we present a systematic survey of PPR protein genes and report on the identification of additional DYW-type PPR proteins in the protists Acanthamoeba castellanii, Malawimonas jakobiformis, and Physarum polycephalum. Moreover, DYW domains were also found in basal branches of multi-cellular lineages outside of land plants, including the alga Nitella flexilis and the rotifers Adineta ricciae and Philodina roseola. Intriguingly, the well-characterized and curious patterns of mitochondrial RNA editing in the slime mold Physarum also include examples of C-to-U changes. Finally, we identify candidate sites for mitochondrial RNA editing in Malawimonas, further supporting a link between DYW-type PPR proteins and C-to-U editing, which may have remained hitherto unnoticed in additional eukaryote lineages.