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Population expansion is a global issue, especially for food production. Meanwhile, global climate change is damaging our soils, making it difficult for crops to thrive and lowering both production and quality. Poor nutrition and salinity stress affect plant growth and development. Although the impact of individual plant stresses has been studied for decades, the real stress scenario is more complex due to the exposure to multiple stresses at the same time. Here we investigate using existing evidence and a meta-analysis approach to determine molecular linkages between 2 contemporaneous abiotic stimuli, phosphate (Pi) deficiency and salinity, on a single plant cell model, the root hairs (RHs), which is the first plant cell exposed to them. Understanding how these 2 stresses work molecularly in RHs may help us build super-adaptable crops and sustainable agriculture in the face of global climate change., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Piscirickettsia salmonis is the most important health problem facing Chilean Aquaculture. Previous reports suggest that P. salmonis can survive in salmonid macrophages by interfering with the host immune response. However, the relevant aspects of the molecular pathogenesis of P. salmonis have been poorly characterized. In this work, we evaluated the transcriptomic changes in macrophage-like cell line SHK-1 infected with P. salmonis at 24- and 48-hours post-infection (hpi) and generated network models of the macrophage response to the infection using co-expression analysis and regulatory transcription factor-target gene information. Transcriptomic analysis showed that 635 genes were differentially expressed after 24- and/or 48-hpi. The pattern of expression of these genes was analyzed by weighted co-expression network analysis (WGCNA), which classified genes into 4 modules of expression, comprising early responses to the bacterium. Induced genes included genes involved in metabolism and cell differentiation, intracellular transportation, and cytoskeleton reorganization, while repressed genes included genes involved in extracellular matrix organization and RNA metabolism. To understand how these expression changes are orchestrated and to pinpoint relevant transcription factors (TFs) controlling the response, we established a curated database of TF-target gene regulatory interactions in Salmo salar , SalSaDB. Using this resource, together with co-expression module data, we generated infection context-specific networks that were analyzed to determine highly connected TF nodes. We found that the most connected TF of the 24- and 48-hpi response networks is KLF17, an ortholog of the KLF4 TF involved in the polarization of macrophages to an M2-phenotype in mammals. Interestingly, while KLF17 is induced by P. salmonis infection, other TFs, such as NOTCH3 and NFATC1, whose orthologs in mammals are related to M1-like macrophages, are repressed. In sum, our results suggest the induction of early regulatory events associated with an M2-like phenotype of macrophages that drives effectors related to the lysosome, RNA metabolism, cytoskeleton organization, and extracellular matrix remodeling. Moreover, the M1-like response seems delayed in generating an effective response, suggesting a polarization towards M2-like macrophages that allows the survival of P. salmonis . This work also contributes to SalSaDB, a curated database of TF-target gene interactions that is freely available for the Atlantic salmon community., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Pérez-Stuardo, Frazão, Ibaceta, Brianson, Sánchez, Rivas-Pardo, Vallejos-Vidal, Reyes-López, Toro-Ascuy, Vidal and Reyes-Cerpa.)

Background: Thigh pain is relatively common after total knee arthroplasty (TKA) and has been attributed to compression of the thigh muscles by the tourniquet used during surgery. Thigh pain that occurs after a TKA that was performed without a tourniquet may be due to a strain of the quadriceps muscle or insertion of the intramedullary (IM) rod. The purpose of the present study was to determine the cause of thigh pain after TKA in a randomized controlled trial evaluating tourniquet use, IM rod use, and quadriceps strain., Methods: This prospective randomized controlled trial enrolled 97 subjects undergoing primary knee arthroplasty into 4 groups according to tourniquet use (yes or no) and IM rod use (yes or no). Quadriceps strain was evaluated with magnetic resonance imaging (MRI) on postoperative day 1 (POD 1). Data collected preoperatively, intraoperatively, and postoperatively until the 6-week clinical visit included pain levels for the knee and thigh (recorded separately) and knee range of motion., Results: Regardless of tourniquet or IM rod use, 73 (75%) of the 97 patients reported thigh pain on POD 1. Thigh pain at 2 weeks postoperatively was indicative of a quadriceps strain. Use of a tourniquet and patient-reported thigh pain at 2 weeks increased the odds of a quadriceps strain, whereas IM rod use did not significantly contribute to thigh pain., Conclusions: The etiology of thigh pain after TKA may be multifactorial; however, an iatrogenic quadriceps strain is one source of thigh pain after TKA, especially if the pain persists 2 weeks after surgery., Level of Evidence: Prognostic Level I . See Instructions for Authors for a complete description of levels of evidence., Competing Interests: Disclosure: The Disclosure of Potential Conflicts of Interest forms are provided with the online version of the article ( http://links.lww.com/JBJS/H381 )., (Copyright © 2023 The Authors. Published by The Journal of Bone and Joint Surgery, Incorporated. All rights reserved.)

Iron is the most abundant micronutrient in plant mitochondria, and it has a crucial role in biochemical reactions involving electron transfer. It has been described in Oryza sativa that Mitochondrial Iron Transporter ( MIT ) is an essential gene and that knockdown mutant rice plants have a decreased amount of iron in their mitochondria, strongly suggesting that OsMIT is involved in mitochondrial iron uptake. In Arabidopsis thaliana , two genes encode MIT homologues. In this study, we analyzed different AtMIT1 and AtMIT2 mutant alleles, and no phenotypic defects were observed in individual mutant plants grown in normal conditions, confirming that neither AtMIT1 nor AtMIT2 are individually essential. When we generated crosses between the Atmit1 and Atmit2 alleles, we were able to isolate homozygous double mutant plants. Interestingly, homozygous double mutant plants were obtained only when mutant alleles of Atmit2 with the T-DNA insertion in the intron region were used for crossings, and in these cases, a correctly spliced AtMIT2 mRNA was generated, although at a low level. Atmit1 Atmit2 double homozygous mutant plants, knockout for AtMIT1 and knockdown for AtMIT2 , were grown and characterized in iron-sufficient conditions. Pleiotropic developmental defects were observed, including abnormal seeds, an increased number of cotyledons, a slow growth rate, pinoid stems, defects in flower structures, and reduced seed set. A RNA-Seq study was performed, and we could identify more than 760 genes differentially expressed in Atmit1 Atmit2 . Our results show that Atmit1 Atmit2 double homozygous mutant plants misregulate genes involved in iron transport, coumarin metabolism, hormone metabolism, root development, and stress-related response. The phenotypes observed, such as pinoid stems and fused cotyledons, in Atmit1 Atmit2 double homozygous mutant plants may suggest defects in auxin homeostasis. Unexpectedly, we observed a possible phenomenon of T-DNA suppression in the next generation of Atmit1 Atmit2 double homozygous mutant plants, correlating with increased splicing of the A tMIT2 intron containing the T-DNA and the suppression of the phenotypes observed in the first generation of the double mutant plants. In these plants with a suppressed phenotype, no differences were observed in the oxygen consumption rate of isolated mitochondria; however, the molecular analysis of gene expression markers, AOX1a , UPOX , and MSM1 , for mitochondrial and oxidative stress showed that these plants express a degree of mitochondrial perturbation. Finally, we could establish by a targeted proteomic analysis that a protein level of 30% of MIT2, in the absence of MIT1, is enough for normal plant growth under iron-sufficient conditions.

LSUs (RESPONSE TO LOW SULFUR) are plant-specific proteins of unknown function that were initially identified during transcriptomic studies of the sulfur deficiency response in Arabidopsis. Recent functional studies have shown that LSUs are important hubs of protein interaction networks with potential roles in plant stress responses. In particular, LSU proteins have been reported to interact with members of the brassinosteroid, jasmonate signaling, and ethylene biosynthetic pathways, suggesting that LSUs may be involved in response to plant stress through modulation of phytohormones. Furthermore, in silico analysis of the promoter regions of LSU genes in Arabidopsis has revealed the presence of cis-regulatory elements that are potentially responsive to phytohormones such as ABA, auxin, and jasmonic acid, suggesting crosstalk between LSU proteins and phytohormones. In this review, we summarize current knowledge about the LSU gene family in plants and its potential role in phytohormone responses.

Here we list species-specific recommendations for housing, care and management of cephalopod molluscs employed for research purposes with the aim of contributing to the standardization of minimum requirements for establishments, care and accommodation of these animals in compliance with the principles stated in Directive 2010/63/EU. Maximizing their psychophysical welfare was our priority. General recommendations on water surface area, water depth and tank shape here reported represent the outcome of the combined action of the analysis of the available literature and an expertise-based consensus reached - under the aegis of the COST Action FA1301 - among researchers working with the most commonly used cephalopod species in Europe. Information on water supply and quality, environmental conditions, stocking density, feeding and handling are also provided. Through this work we wish to set the stage for a more fertile ground of evidence-based approaches on cephalopod laboratory maintenance, thus facilitating standardization and replicability of research outcomes across laboratories, at the same time maximizing the welfare of these animals.

RNA interference is an ancient mechanism with many regulatory roles in eukaryotic genomes, with small RNAs acting as their functional element. While there is a wide array of classes of small-RNA-producing loci, those resulting from stem-loop structures (hairpins) have received profuse attention. Such is the case of microRNAs (miRNAs), which have distinct roles in plants and animals. Fungi also produce small RNAs, and several publications have identified miRNAs and miRNA-like (mi/milRNA) hairpin RNAs in diverse fungal species using deep sequencing technologies. Despite this relevant source of information, relatively little is known about mi/milRNA features in fungi, mostly due to a lack of established criteria for their annotation. To systematically assess mi/milRNA characteristics and annotation confidence, we searched for publications describing mi/milRNA loci and re-assessed the annotations for 41 fungal species. We extracted and normalized the annotation data for 1727 reported mi/milRNA loci and determined their abundance profiles, concluding that less than half of the reported loci passed basic standards used for hairpin RNA discovery. We found that fungal mi/milRNA are generally more similar in size to animal miRNAs and were frequently associated with protein-coding genes. The compiled genomic analyses identified 25 mi/milRNA loci conserved in multiple species. Our pipeline allowed us to build a general hierarchy of locus quality, identifying more than 150 loci with high-quality annotations. We provide a centralized annotation of identified mi/milRNA hairpin RNAs in fungi which will serve as a resource for future research and advance in understanding the characteristics and functions of mi/milRNAs in fungal organisms., Competing Interests: NJ, JÁ, EV No competing interests declared, LL Reviewing editor, eLife, (© 2022, Johnson et al.)

MicroRNAs (miRNAs) are small noncoding RNAs that are key players in the regulation of gene expression. In the past decade, with the increasing accessibility of high-throughput sequencing technologies, different methods have been developed to identify miRNAs, most of which rely on preexisting reference genomes. However, when a reference genome is absent or is not of high quality, such identification becomes more difficult. In this context, we developed BrumiR, an algorithm that is able to discover miRNAs directly and exclusively from small RNA (sRNA) sequencing (sRNA-seq) data. We benchmarked BrumiR with datasets encompassing animal and plant species using real and simulated sRNA-seq experiments. The results demonstrate that BrumiR reaches the highest recall for miRNA discovery, while at the same time being much faster and more efficient than the state-of-the-art tools evaluated. The latter allows BrumiR to analyze a large number of sRNA-seq experiments, from plants or animal species. Moreover, BrumiR detects additional information regarding other expressed sequences (sRNAs, isomiRs, etc.), thus maximizing the biological insight gained from sRNA-seq experiments. Additionally, when a reference genome is available, BrumiR provides a new mapping tool (BrumiR2reference) that performs an a posteriori exhaustive search to identify the precursor sequences. Finally, we also provide a machine learning classifier based on a random forest model that evaluates the sequence-derived features to further refine the prediction obtained from the BrumiR-core. The code of BrumiR and all the algorithms that compose the BrumiR toolkit are freely available at https://github.com/camoragaq/BrumiR., (© The Author(s) 2022. Published by Oxford University Press GigaScience.)

LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein-protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta -specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta -specific gene family and their response to S deficiency is conserved in angiosperms.

Iron is an essential micronutrient for humans and other organisms. Its deficiency is one of the leading causes of anemia worldwide. The world health organization has proposed that an alternative to increasing iron content in food is through crop biofortification. One of the most consumed part of crops is the seed, however, little is known about how iron accumulation in seed occurs and how it is regulated. B3 transcription factors play a critical role in the accumulation of storage compounds such as proteins and lipids. Their role in seed maturation has been well characterized. However, their relevance in accumulation and distribution of micronutrients like iron remains unknown. In Arabidopsis thaliana and other plant models, three master regulators belonging to the B3 transcription factors family have been identified: FUSCA3 (FUS3), LEAFY COTYLEDON2 (LEC2), and ABSCISIC ACID INSENSITIVE 3 (ABI3). In this work, we studied how seed iron homeostasis is affected in B3 transcription factors mutants using histological and molecular approaches. We determined that iron distribution is modified in abi3 , lec2 , and fus3 embryo mutants. For abi3-6 and fus3-3 mutant embryos, iron was less accumulated in vacuoles of cells surrounding provasculature compared with wild type embryos. lec2-1 embryos showed no difference in the pattern of iron distribution in hypocotyl, but a dramatic decrease of iron was observed in cotyledons. Interestingly, for the three mutant genotypes, total iron content in dry mutant seeds showed no difference compared to wild type. At the molecular level, we showed that genes encoding the iron storage ferritins proteins are misregulated in mutant seeds. Altogether our results support a role of the B3 transcription factors ABI3, LEC2, and FUS3 in maintaining iron homeostasis in Arabidopsis embryos., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Grant-Grant, Schaffhauser, Baeza-Gonzalez, Gao, Conéjéro, Vidal, Gaymard, Dubos, Curie and Roschzttardtz.)

Background: Reverse shoulder arthroplasty (RSA) has been shown to reliably improve pain and functional outcomes for multiple pathologies. Despite its increasing use in the United States since its introduction in 2004, few studies have investigated long-term outcomes of this procedure. This information is vital in many ways, including durability of functional outcomes, complication profiles, and implant survivorship., Methods: Our prospectively collected shoulder arthroplasty registry included 471 patients who had undergone RSA prior to December 31, 2010, by a single surgeon at a high-volume shoulder arthroplasty center. The study sample included 94 patients with a minimum of 10 years' follow-up, and we evaluated the indications for RSA, complications, pain, Single Assessment Numeric Evaluation (SANE), and patient satisfaction on these patients at baseline, 2-5 years, and 10 or more years of follow-up. Prosthesis survivorship was determined by Kaplan-Meier survival analysis performed with revision for any reason as the end point for all 471 patients in the study period regardless of follow-up interval., Results: The 93 patients with at least 10 years of follow-up were 63% female (60) and 37% male (34), with an average age of 66±10 years at the time of RSA. There were 70 (75%) primary RSAs and 23 (25%) revision RSAs. Patient-reported outcome measures at 10 years or more included a current pain rating averaging 2±3 on a 0-10 scale and Single Assessment Numeric Evaluation (SANE) of 73±28. There was no deterioration in function or pain from midterm to long-term follow-up, as the SANE and pain score changed by less than the minimal clinically important difference or improved in 87% and 90% of patients, respectively. Overall, patients were satisfied with the RSA procedure, with 52 (56%) very satisfied, 24 (26%) satisfied, 13 (14%) dissatisfied, and 4 (4%) very dissatisfied. For the subset of 68 patients who were contacted for follow-up, 64 (94%) would have the procedure again and 4 (6%) would not. Kaplan-Meier prosthesis survival rate for all 471 RSA patients was 88% (95% confidence interval [CI] 84%-92%) at 5 years and 81% (95% CI 74%-86%) at 10 years., Conclusions: This study presents the largest American cohort of Grammont design RSA at a minimum 10-year follow-up. Although RSA provided clinically significant and durable improvements in pain and function, the complication and revision rates were higher than prior reports. Despite this, the vast majority of patients were satisfied and would have the procedure again., (Copyright © 2021 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.)

Nitrate is a nutrient and a potent signal that impacts global gene expression in plants. However, the regulatory factors controlling temporal and cell type-specific nitrate responses remain largely unknown. We assayed nitrate-responsive transcriptome changes in five major root cell types of the Arabidopsis thaliana root as a function of time. We found that gene-expression response to nitrate is dynamic and highly localized and predicted cell type-specific transcription factor (TF)-target interactions. Among cell types, the endodermis stands out as having the largest and most connected nitrate-regulatory gene network. ABF2 and ABF3 are major hubs for transcriptional responses in the endodermis cell layer. We experimentally validated TF-target interactions for ABF2 and ABF3 by chromatin immunoprecipitation followed by sequencing and a cell-based system to detect TF regulation genome-wide. Validated targets of ABF2 and ABF3 account for more than 50% of the nitrate-responsive transcriptome in the endodermis. Moreover, ABF2 and ABF3 are involved in nitrate-induced lateral root growth. Our approach offers an unprecedented spatiotemporal resolution of the root response to nitrate and identifies important components of cell-specific gene regulatory networks., Competing Interests: The authors declare no competing interest., (Copyright © 2022 the Author(s). Published by PNAS.)

Transcription and processing of 45S rRNAs in the nucleolus are keystones of ribosome biogenesis. While these processes are severely impacted by stress conditions in multiple species, primarily upon heat exposure, we lack information about the molecular mechanisms allowing sessile organisms without a temperature-control system, like plants, to cope with such circumstances. We show that heat stress disturbs nucleolar structure, inhibits pre-rRNA processing and provokes imbalanced ribosome profiles in Arabidopsis thaliana plants. Notably, the accuracy of transcription initiation and cleavage at the primary P site in the 5'ETS (5' External Transcribed Spacer) are not affected but the levels of primary 45S and 35S transcripts are, respectively, increased and reduced. In contrast, precursors of 18S, 5.8S and 25S RNAs are rapidly undetectable upon heat stress. Remarkably, nucleolar structure, pre-rRNAs from major ITS1 processing pathway and ribosome profiles are restored after returning to optimal conditions, shedding light on the extreme plasticity of nucleolar functions in plant cells. Further genetic and molecular analysis to identify molecular clues implicated in these nucleolar responses indicate that cleavage rate at P site and nucleolin protein expression can act as a checkpoint control towards a productive pre-rRNA processing pathway.

Botrytis cinerea and Trichoderma atroviride are two relevant fungi in agricultural systems. To gain insights into these organisms' transcriptional gene regulatory networks (GRNs), we generated a manually curated transcription factor (TF) dataset for each of them, followed by a GRN inference utilizing available sequence motifs describing DNA-binding specificity and global gene expression data. As a proof of concept of the usefulness of this resource to pinpoint key transcriptional regulators, we employed publicly available transcriptomics data and a newly generated dual RNA-seq dataset to build context-specific Botrytis and Trichoderma GRNs under two different biological paradigms: exposure to continuous light and Botrytis-Trichoderma confrontation assays. Network analysis of fungal responses to constant light revealed striking differences in the transcriptional landscape of both fungi. On the other hand, we found that the confrontation of both microorganisms elicited a distinct set of differentially expressed genes with changes in T. atroviride exceeding those in B. cinerea . Using our regulatory network data, we were able to determine, in both fungi, central TFs involved in this interaction response, including TFs controlling a large set of extracellular peptidases in the biocontrol agent T. atroviride . In summary, our work provides a comprehensive catalog of transcription factors and regulatory interactions for both organisms. This catalog can now serve as a basis for generating novel hypotheses on transcriptional regulatory circuits in different experimental contexts., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

Background: In counseling patients about the complications of revision total hip arthroplasty (revTHA), it is imperative that mortality be considered. The actual mortality rate by indication of revision is ill-defined. The purpose of this study is to determine the mortality rate after revTHA., Methods: An institutional database identified 596 patients who had undergone revTHA between 2012 and 2018. Medical records, national, state, and local death indexes were queried for mortality status and indication for revTHA. For survivors, the last clinical visit date was used for censoring in the mortality analysis. Mortality rates were calculated for all clinical patients and then by specific indication for revision., Results: The overall 2-year mortality rate following revTHA was 19.5 deaths per 1000 or 1 in 51 patients. Patients presenting with a periprosthetic fracture had a significantly higher 2-year mortality rate of 74.5 deaths per 1000 or 1 in 13 patients (P < .001), while an indication of dislocation or instability had a slightly higher 2-year mortality rate of 50.3 per 1000 (1 in 20) but this difference was not significant (P = .531). Other indications such as mechanical loosening or infection did not have a significantly different mortality rate., Conclusion: The overall 2-year mortality rate following revTHA was 19.5 deaths per 1000 which was largely attributed to patients with a periprosthetic fracture (74.5 per 1000) with other indications not significantly impacting mortality. Mortality rates and specific rates by indication for revision should be considered when counseling patients prior to revTHA., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription-PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

During mating, males provide not only the spermatozoa to fertilize the oocyte but also other stimuli that are essential for initiating and maintaining the reproductive programme in females. In the mammalian oviduct, mating regulates sperm storage, egg transport, fertilization, early embryonic development, and oestradiol metabolism. However, the main molecules underlying these processes are poorly understood. Using microarray analyses, we identified 58 genes that were either induced or repressed by mating in the endosalpinx at 3 h post-stimulus. RT-qPCR confirmed that mating downregulated the expression of the Oas1h and Prim1 genes and upregulated the expression of the Ceacam1, Chad, Chst10, Slc5a3 and Slc26a4 genes. The functional category 'cell-to-cell signalling and interaction' was over-represented in this gene list. Network modelling identified TNF and all-trans retinoic acid (RA) as upstream regulators of the mating-induced transcriptional response, which was confirmed by intraoviductal injection of TNF or RA in unmated rats. It partially mimicked the transcriptional effect of mating in the rat endosalpinx. Furthermore, mating decreased RA levels in oviductal fluid, and RA-receptor-gamma (RARG) exhibited a nuclear location in oviductal epithelium in both unmated and mated rats, indicating RA-RARG transcriptional activity. In conclusion, the early transcriptional response regulated by mating in the rat endosalpinx is mediated by TNF and RA. These signalling molecules regulate a cohort of genes involved in 'cell-to-cell signalling and interactions' and merit further studies to understand the specific processes activated in the endosalpinx to sustain the events that occur in the mammalian oviduct early after mating.

Purpose: The purpose of this study was to evaluate whether fellowship training affected trends and complications of operative clavicle fracture treatment in newly trained orthopedic surgeons., Methods: The American Board of Orthopedic Surgery (ABOS) database was utilized to identify cases of open treatment of clavicle fractures submitted by ABOS Part-II Board Certification candidates. From 2005 to 2017, 3148 candidates performed at least one open clavicle fracture treatment. Overall, 6919 cases were included; 3516 of these had over 6 weeks of follow-up. Candidates were divided by fellowship type into 5 groups: Trauma, Sports Medicine, Hand and Upper Extremity or Shoulder, multiple, and other or no fellowship(s). Group differences were analyzed with ANOVA and Bonferroni post hoc analysis. Complications, reoperations, nonunion rates, and readmissions between groups were evaluated with Chi-squared test and logistic regression analyses., Results: Case volume during the study period was significantly higher after 2007. Trauma candidates performed significantly more operations for clavicle fracture per candidate while candidates with other or no fellowship(s) performed significantly fewer operations per candidate. Patients treated by Trauma candidates were significantly older, had significantly fewer early surgical complications and significantly more early medical complications. Nonunion rates were not significantly different between groups., Conclusion: Candidates treated clavicle fractures surgically more often in 2007 and beyond. Trauma candidates treated older patients, had fewer early surgical complications, and had more medical complications. Reoperation, readmission and nonunion rates were not significantly different between groups., (© 2020 Delhi Orthopedic Association. All rights reserved.)

Background: Sulfur is a major component of biological molecules and thus an essential element for plants. Deficiency of sulfate, the main source of sulfur in soils, negatively influences plant growth and crop yield. The effect of sulfate deficiency on plants has been well characterized at the physiological, transcriptomic and metabolomic levels in Arabidopsis thaliana and a limited number of crop plants. However, we still lack a thorough understanding of the molecular mechanisms and regulatory networks underlying sulfate deficiency in most plants. In this work we analyzed the impact of sulfate starvation on the transcriptome of tomato plants to identify regulatory networks and key transcriptional regulators at a temporal and organ scale., Results: Sulfate starvation reduces the growth of roots and leaves which is accompanied by major changes in the organ transcriptome, with the response being temporally earlier in roots than leaves. Comparative analysis showed that a major part of the Arabidopsis and tomato transcriptomic response to sulfate starvation is conserved between these plants and allowed for the identification of processes specifically regulated in tomato at the transcript level, including the control of internal phosphate levels. Integrative gene network analysis uncovered key transcription factors controlling the temporal expression of genes involved in sulfate assimilation, as well as cell cycle, cell division and photosynthesis during sulfate starvation in tomato roots and leaves. Interestingly, one of these transcription factors presents a high identity with SULFUR LIMITATION1, a central component of the sulfate starvation response in Arabidopsis., Conclusions: Together, our results provide the first comprehensive catalog of sulfate-responsive genes in tomato, as well as novel regulatory targets for future functional analyses in tomato and other crops.

Nitrogen (N) is an essential macronutrient for plants and a major limiting factor for plant growth and crop production. Nitrate is the main source of N available to plants in agricultural soils and in many natural environments. Sustaining agricultural productivity is of paramount importance in the current scenario of increasing world population, diversification of crop uses, and climate change. Plant productivity for major crops around the world, however, is still supported by excess application of N-rich fertilizers with detrimental economic and environmental impacts. Thus, understanding how plants regulate nitrate uptake and metabolism is key for developing new crops with enhanced N use efficiency and to cope with future world food demands. The study of plant responses to nitrate has gained considerable interest over the last 30 years. This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology. We discuss how we have reached our current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants. We hope this summary will serve not only as a timeline and information repository but also as a baseline to define outstanding questions for future research., (© 2020 American Society of Plant Biologists. All rights reserved.)

Background: Total shoulder arthroplasty (TSA) with an anatomic or reverse prosthesis is a commonly used and successful treatment option for many degenerative shoulder conditions. There is an increasing trend toward fellowship training and subspecialization in newly trained orthopedic surgeons. The literature also suggests that subspecialization and high volume are associated with better clinical outcomes. The purpose of this study was to evaluate the effects of fellowship training on the trends and outcomes of TSA in board-eligible orthopedic surgeons., Methods: The American Board of Orthopaedic Surgery database was used to identify primary TSA cases performed for osteoarthrosis submitted by American Board of Orthopaedic Surgery Part II Board Certification candidates. Candidates were grouped based on fellowship training and subspecialty examination being taken. Groups were analyzed with analysis of variance and Bonferroni post hoc analysis to evaluate significant differences between groups for a number of candidates, cases per candidate, and patient age/sex. Differences in complications, reoperations, and readmissions were statistically evaluated with χ 2  tests and multivariate logistic regression analysis., Results: From 2010 to 2017, 854 candidates performed at least 1 primary TSA (anatomic or reverse) after a diagnosis of osteoarthritis and 2720 submitted cases met inclusion criteria. Candidates completing a Shoulder fellowship performed significantly more TSAs per candidate compared with all other groups (Shoulder = 8.0 ± 6.2, Sports Medicine = 2.4 ± 2.1, Hand and Upper Extremity = 2.9 ± 2.9, General Orthopedics = 2.4 ± 2.3, P < .001). The Shoulder fellowship group had significantly lower complication rates (17.9%) as compared with the Sports Medicine fellowship (23.7%, P = .008) and Hand and Upper Extremity fellowship (25.0%, P = .008) groups., Conclusions: Shoulder fellowship-trained surgeons performed significantly more TSAs per year than other groups, with a lower complication rate when compared with other fellowship-trained candidates. Fellowship type had no effect on reoperation or readmission rates., (Copyright © 2019 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.)

Introduction: Delays for consultation of more than six months exist for uterine cancer. Delays in diagnosis of more than five years exist for vulvar cancer. The peak incidence of these neoplasms appear after the age of 65 years. Patient's symptoms are characteristically swelling, vaginal bleeding or itching. This study aims to understand what is happening during this period for women over 65 years old. It also tries to identify triggers during the help-seeking period., Methods: Qualitative studies using semi-structured interviews with dual analyses (semio-pragmatic and psychodynamic) have been conducted on a population of older (65+) gynaecologic cancer patients, recruited from a French oncology centre., Results: Twelve patients were interviewed. Patients' courses of action were determined by the characteristics of their symptoms, their feelings and their emotions. Representations, subjective beliefs and past experiences were employed to make sense of their symptoms. The patient's friend and family circle had an important role in incentivizing the patient to seek consultation. Multiple factors affected the path towards consulting the doctor. The initial medical contact included several challenges. The patient would consult a doctor earlier if he had more information about his illness and if his relationship with the doctor was better., Conclusion: Our findings are similar to those of other cancers. The peculiarity for this population appears to be the different representations of age-related changes in the reproductive system, and the taboo associated with this issue when facing friends and family., (Copyright © 2019 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.)

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 6 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.

Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology, and neurogenesis in the adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits. Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress on the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our in silico study identified the top-10 biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development and function, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our in silico study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress.

The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely regulated by the integration of an array of environmental and endogenous factors. Nitrogen is the mineral macronutrient that plants require in the largest amount, and as such its availability greatly impacts on many aspects of plant growth and development, including flowering time. We found that nitrate signaling interacts with the age-related and gibberellic acid pathways to control flowering time in Arabidopsis thaliana. We revealed that repressors of flowering time belonging to the AP2-type transcription factor family including SCHLAFMUTZE (SMZ) and SCHNARCHZAPFEN (SNZ) are important regulators of flowering time in response to nitrate. Our results support a model whereby nitrate activates SMZ and SNZ via the gibberellin pathway to repress flowering time in Arabidopsis thaliana., (© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Summary: GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve several interacting processes. GENIUS also enriches the network with new genes related to the biological function of interest, with accuracies comparable to highly discriminative Support Vector Machine methods., Availability and Implementation: GENIUS currently supports eight model organisms and is freely available for public use at http://networks.bio.puc.cl/genius ., Contact: genius.psbl@gmail.com., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press.)

Cephalopods (nautiluses, cuttlefishes, squids and octopuses) exhibit direct development and display two major developmental modes: planktonic and benthic. Planktonic hatchlings are small and go through some degree of morphological changes during the planktonic phase, which can last from days to months, with ocean currents enhancing their dispersal capacity. Benthic hatchlings are usually large, miniature-like adults and have comparatively reduced dispersal potential. We examined the relationship between early developmental mode, hatchling size and species latitudinal distribution range of 110 species hatched in the laboratory, which represent 13% of the total number of live cephalopod species described to date. Results showed that species with planktonic hatchlings reach broader distributional ranges in comparison with species with benthic hatchlings. In addition, squids and octopods follow an inverse relationship between hatchling size and species latitudinal distribution. In both groups, species with smaller hatchlings have broader latitudinal distribution ranges. Thus, squid and octopod species with larger hatchlings have latitudinal distributions of comparatively minor extension. This pattern also emerges when all species are grouped by genus (n = 41), but was not detected for cuttlefishes, a group composed mainly of species with large and benthic hatchlings. However, when hatchling size was compared to adult size, it was observed that the smaller the hatchlings, the broader the latitudinal distributional range of the species for cuttlefishes, squids and octopuses. This was also valid for all cephalopod species with benthic hatchlings pooled together. Hatchling size and associated developmental mode and dispersal potential seem to be main influential factors in determining the distributional range of cephalopods., Competing Interests: The authors have declared that no competing interests exist.

Development of crops with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. However, achieving this goal has proven difficult since NUE is a complex trait encompassing physiological and developmental processes. We thought to tackle this problem by taking a systems biology approach to identify candidate target genes. First, we used a supervised machine-learning algorithm to predict a NUE gene network in Arabidopsis (Arabidopsis thaliana). Second, we identified BT2, a member of the Bric-a-Brac/Tramtrack/Broad gene family, as the most central and connected gene in the NUE network. Third, we experimentally tested BT2 for a role in NUE. We found NUE decreased in plants overexpressing BT2 gene compared to wild-type plants under limiting nitrate conditions. In addition, NUE increased compared to wild-type plants under low nitrate conditions in double mutant plants in bt2 and its closely related homolog bt1, indicating a functional redundancy of BT1 and BT2 for NUE. Expression of the nitrate transporter genes NRT2.1 and NRT2.4 increased in the bt1/bt2 double mutant compared to wild-type plants, with a concomitant 65% increase in nitrate uptake under low nitrate conditions. Similar to Arabidopsis, we found that mutation of the BT1/BT2 ortholog gene in rice (Oryza sativa) OsBT increased NUE by 20% compared to wild-type rice plants under low nitrogen conditions. These results indicate BT gene family members act as conserved negative regulators of nitrate uptake genes and NUE in plants and highlight them as prime targets for future strategies to improve NUE in crops., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Background: Intestinal malrotation is a rare congenital anomaly. In adults is very difficult to recognize due to the lack of symptoms. Diagnosis is usually incidental during surgical procedures or at autopsy., Aim: To review the occurrence and recognition of uneventful intestinal malrotation discovered during regular cases of bariatric surgeries., Methods: Were retrospectively reviewed the medical registry of 20,000 cases undergoing bariatric surgery, from January 2002 to January 2016, looking for the occurrence of intestinal malrotation and consequences in the intraoperative technique and immediate evolution of the patients., Results: Five cases (0,025%) of intestinal malrotation were found. All of them were males, aging 45, 49, 37,52 and 39 years; BMI 35, 42, 49, 47 and 52 kg/m2, all of them with a past medical history of morbid obesity. The patient with BMI 35 kg/m2 suffered from type 2 diabetes also. All procedures were completed by laparoscopic approach, with no conversions. In one patient was not possible to move the jejunum to the upper abdomen in order to establish the gastrojejunostomy and a sleeve gastrectomy was performed. In another patient was not possible to fully recognize the anatomy due to bowel adhesions and a single anastomosis gastric bypass was preferred. No leaks or bleeding were identified. There were no perioperative complications. All patients were discharged 72 h after the procedure and no immediate 30-day complications were reported., Conclusion: Patients with malrotation can successfully undergo laparoscopic bariatric surgery. May be necessary changes in the surgical original strategy regarding the malrotation. Surgeons must check full abdominal anatomical condition prior to start the division of the stomach., Competing Interests: none

Nitrogen is an essential macronutrient for plants and its availability is a key determinant of plant growth and development and crop yield. Besides their nutritional role, N nutrients and metabolites are signals that activate signaling pathways that modulate many plant processes. Because the most abundant inorganic N source for plants in agronomic soils is nitrate, much of the work to understand plant N-signaling has focused on this nutrient. Over the last years, several studies defined a comprehensive catalog of nitrate-responsive genes, involved in nitrate transport, metabolism and a variety of other processes. Despite significant progress in recent years, primarily using Arabidopsis thaliana as a model system, the molecular mechanisms by which nitrate elicits changes in transcript abundance are still not fully understood. Here we highlight recent advancements in identifying key transcription factors and transcriptional mechanisms that orchestrate the gene expression response to changes in nitrate availability in A. thaliana., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Understanding how plants sense and respond to changes in nitrogen availability is the first step toward developing strategies for biotechnological applications, such as improvement of nitrogen use efficiency. However, components involved in nitrogen signaling pathways remain poorly characterized. Calcium is a second messenger in signal transduction pathways in plants, and it has been indirectly implicated in nitrate responses. Using aequorin reporter plants, we show that nitrate treatments transiently increase cytoplasmic Ca(2+) concentration. We found that nitrate also induces cytoplasmic concentration of inositol 1,4,5-trisphosphate. Increases in inositol 1,4,5-trisphosphate and cytoplasmic Ca(2+) levels in response to nitrate treatments were blocked by U73122, a pharmacological inhibitor of phospholipase C, but not by the nonfunctional phospholipase C inhibitor analog U73343. In addition, increase in cytoplasmic Ca(2+) levels in response to nitrate treatments was abolished in mutants of the nitrate transceptor NITRATE TRANSPORTER1.1/Arabidopsis (Arabidopsis thaliana) NITRATE TRANSPORTER1 PEPTIDE TRANSPORTER FAMILY6.3. Gene expression of nitrate-responsive genes was severely affected by pretreatments with Ca(2+) channel blockers or phospholipase C inhibitors. These results indicate that Ca(2+) acts as a second messenger in the nitrate signaling pathway of Arabidopsis. Our results suggest a model where NRT1.1/AtNPF6.3 and a phospholipase C activity mediate the increase of Ca(2+) in response to nitrate required for changes in expression of prototypical nitrate-responsive genes., (© 2015 American Society of Plant Biologists. All Rights Reserved.)

Technological advances in the last decade have enabled biologists to produce increasing amounts of information for the transcriptome, proteome, interactome, and other -omics data sets in many model organisms. A major challenge is integration and biological interpretation of these massive data sets in order to generate testable hypotheses about gene regulatory networks or molecular mechanisms that govern system behaviors. Constructing gene networks requires bioinformatics skills to adequately manage, integrate, analyze and productively use the data to generate biological insights. In this chapter, we provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape platforms. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.

Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Nitrate acts as a potent signal to control global gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly after nitrate treatments in roots. Global gene expression analysis revealed 97% of the genes with altered expression in tga1 tga4 double mutant plants respond to nitrate treatments, indicating that these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. We found TGA1 and TGA4 regulate the expression of nitrate transporter genes NRT2.1 and NRT2.2. Specific binding of TGA1 to its cognate DNA sequence on NRT2.1 and NRT2.2 promoters was confirmed by chromatin immunoprecipitation assays. The tga1 tga4 double mutant plants exhibit nitrate-dependent lateral and primary root phenotypes. Lateral root initiation is affected in both tga1 tga4 and nrt1.2 nrt2.2 double mutants, suggesting TGA1 and TGA4 regulate lateral root development at least partly via NRT2.1 and NRT2.2. Additional root phenotypes of tga1 tga4 double mutants indicate that these transcription factors play an important role in root developmental responses to nitrate. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)

Nitrogen is an essential macronutrient for plants and its availability is a major limiting factor for plant growth and crop production. Nitrate is the main source of inorganic N for plants in aerobic soils and can act as a potent signal to control global gene expression. We found that gene expression in response to nitrate treatment of the AFB3 auxin receptor and its target, the NAC4 transcription factor depends on the nitrate transport function of NRT1.1. This gene regulatory function of NRT1.1 on AFB3 and NAC4 differs from the previously described signaling function controlling NRT2.1, NIA1 and NIA2 transcript levels and root colonization of nitrate-rich patches. Our work suggests two different signaling pathways may exist to control gene expression in response to nitrate downstream of NRT1.1.

A recent revival in using cephalopods as experimental animals has rekindled interest in their biology and life cycles, information with direct applications also in the rapidly growing ornamental aquarium species trade and in commercial aquaculture production for human consumption. Cephalopods have high rates of growth and food conversion, which for aquaculture translates into short culture cycles, high ratios of production to biomass and high cost-effectiveness. However, at present, only small-scale culture is possible and only for a few species: the cuttlefish Sepia officinalis, the loliginid squid Sepioteuthis lessoniana and the octopuses Octopus maya and O. vulgaris. These four species are the focus of this chapter, the aims of which are as follows: (1) to provide an overview of the culture requirements of cephalopods, (2) to highlight the physical and nutritional requirements at each phase of the life cycle regarded as essential for successful full-scale culture and (3) to identify current limitations and the topics on which further research is required. Knowledge of cephalopod culture methods is advanced, but commercialization is still constrained by the highly selective feeding habits of cephalopods and their requirement for large quantities of high-quality (preferably live) feed, particularly in the early stages of development. Future research should focus on problems related to the consistent production of viable numbers of juveniles, the resolution of which requires a better understanding of nutrition at all phases of the life cycle and better broodstock management, particularly regarding developments in genetic selection, control of reproduction and quality of eggs and offspring., (© 2014 Elsevier Ltd All rights reserved.)

Background: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out., Results: In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3., Conclusions: Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.

Auxin is a key phytohormone regulating central processes in plants. Although the mechanism by which auxin triggers changes in gene expression is well understood, little is known about the specific role of the individual members of the TIR1/AFB auxin receptors, Aux/IAA repressors, and ARF transcription factors and/or molecular pathways acting downstream leading to plant responses to the environment. We previously reported a role for AFB3 in coordinating primary and lateral root growth to nitrate availability. In this work, we used an integrated genomics, bioinformatics, and molecular genetics approach to dissect regulatory networks acting downstream of AFB3 that are activated by nitrate in roots. We found that the NAC4 transcription factor is a key regulatory element controlling a nitrate-responsive network, and that nac4 mutants have altered lateral root growth but normal primary root growth in response to nitrate. This finding suggests that AFB3 is able to activate two independent pathways to control root system architecture. Our systems approach has unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate.

Nitrogen (N) is an essential macronutrient and a signal that has profound impacts on plant growth and development. In order to cope with changing N regimes in the soil, plants have developed complex regulatory mechanisms that involve short-range and long-range signaling pathways. These pathways act at the cellular and whole plant scale to coordinate plant N metabolism, growth and development according to external and internal N status. Although molecular components of local and systemic N signaling have been identified and characterized, an integrated view of how plants coordinate and organize the N response is still lacking. In this review, we discuss recent advances toward understanding the mechanisms of local and systemic N responses and provide an integrated model for how these responses are orchestrated., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Nitrogen (N) is an essential macronutrient for plants. In nature, N cycles between different inorganic and organic forms some of which can serve as nutrients for plants. The inorganic N forms nitrate and ammonium are the most important sources of N for plants. However, plants can also uptake and use organic N forms such as amino acids and urea. Besides their nutritional role, nitrate and other forms of N can also act as signals that regulate the expression of hundreds of genes causing modulation of plant metabolism, physiology, growth, and development. Although many genes and processes affected by changes in external or internal N have been identified, the molecular mechanisms involved in N sensing and signaling are still poorly understood. Classic reverse and forward genetics and more recently the advent of genomic and systems approaches have helped to characterize some of the components of the signaling pathways directing Arabidopsis responses to N. Here, we provide an update on recent advances to identify the components involved in N sensing and signaling in Arabidopsis and their importance for the plant response to N., (© 2010 John Wiley & Sons, Inc.)

One of the most striking examples of plant developmental plasticity to changing environmental conditions is the modulation of root system architecture (RSA) in response to nitrate supply. Despite the fundamental and applied significance of understanding this process, the molecular mechanisms behind nitrate-regulated changes in developmental programs are still largely unknown. Small RNAs (sRNAs) have emerged as master regulators of gene expression in plants and other organisms. To evaluate the role of sRNAs in the nitrate response, we sequenced sRNAs from control and nitrate-treated Arabidopsis seedlings using the 454 sequencing technology. miR393 was induced by nitrate in these experiments. miR393 targets transcripts that code for a basic helix-loop-helix (bHLH) transcription factor and for the auxin receptors TIR1, AFB1, AFB2, and AFB3. However, only AFB3 was regulated by nitrate in roots under our experimental conditions. Analysis of the expression of this miR393/AFB3 module, revealed an incoherent feed-forward mechanism that is induced by nitrate and repressed by N metabolites generated by nitrate reduction and assimilation. To understand the functional role of this N-regulatory module for plant development, we analyzed the RSA response to nitrate in AFB3 insertional mutant plants and in miR393 overexpressors. RSA analysis in these plants revealed that both primary and lateral root growth responses to nitrate were altered. Interestingly, regulation of RSA by nitrate was specifically mediated by AFB3, indicating that miR393/AFB3 is a unique N-responsive module that controls root system architecture in response to external and internal N availability in Arabidopsis.

Background: The incidence of deep venous thrombosis is 0.6/1000 habitants and when symptomatic its diagnosis by duplex scan has 100% sensitivity and 98% specificity., Objectives: The aim of this study was to evaluate the findings of the duplex scan in patients with clinical suspicion of deep venous thrombosis., Methods: 239 consecutive outpatients (59.2 +/- 18.6 years, 164 female) were evaluated by duplex scan., Results: According to symptoms 101 (42.3%) were related to the right lower limb; 113 (47.3%) to the left lower limb; and 25 were related to both lower limbs. Forty-eight patients presented a normal duplex scan. Venous thrombosis was found in 117 patients (0.49; CI 0.43-0.55): 75 with deep venous thrombosis (DVT), 22 with superficial venous thrombosis (SVT) and 20 with both DVT and SVT. Other pathologies were found in 74 patients. Among patients with DVT the most involved veins were below the knee. Among patients with SVT, 20 (47.6%) showed progression to the deep venous system: 9 (45%) by perforans veins; in 6 by saphenous-femoral junction (30%); and in 5 (25%) by saphenous-popliteal junction., Conclusion: Deep venous and superficial venous thromboses were diagnosed in 49% of cases. In 30.9% of cases, the duplex scan indicated other pathologies.

Objectives: To describe the findings and evaluate appropriateness of a carotid artery study including the measurement of IMT, the presence of atherosclerotic plaque, and their correlation with cardiovascular risk factors., Methods: 555 patients (220 men; 67.06 +/- 12.44 years) were included in the study. 120 patients (21.62%) presented carotid plaque: 108 (19.45%) in patients with at least one risk factor and 12 (2.1%) in patients without risk factors. With respect to appropriateness of the present studies: 65% were appropriate, 22% were uncertain and 13% were inappropriate. The IMT medians were higher in males (0.0280; 95% CI, 00.82 to 0.478; p = 0.0057) and in hypertensive patients (0.391; 95% CI, 0.0190 to 0.0592; p = 0,001). There was a linear increase in mean IMT for each year increased in age (0.0059; 95% CI; 0.0050 to 0.0067). Carotid plaque was more frequent in patients with CAD (p = 0.0002), diabetes (p = 0.024) and hypertension (p = 0.036)., Conclusion: Assessment of carotid arteries identified increased incidence of plaque in patients with CAD, diabetes and hypertension. IMT was increased in older patients, hypertensive patients and males. Forty-five percent of the patients were studied based on uncertain and inappropriate reasons.

Nitrogen (N) is an essential macronutrient available to plants mainly as nitrate in agricultural soils. Besides its role as a nutrient, inorganic and organic N sources play key roles as signals that control genome-wide gene expression in Arabidopsis and other plant species. Genomics approaches have provided us with thousands of genes whose expression is modulated in response to N treatments in Arabidopsis. Recently, systems approaches have been utilized to map the complex molecular network that plants utilize to integrate metabolic, cellular, and developmental processes to successfully adapt to changing N availability. The challenge now is to understand the molecular mechanisms underlying N regulation of gene networks and bridge the gap between N sensing, signaling, and downstream physiological and developmental changes. We discuss recent advances in this direction.