Association between metabolic syndrome and salivary MMP-8, myeloperoxidase in periodontitis.

OBJECTIVE: This study investigated the effect of metabolic syndrome (MetS) on periodontal clinical parameters and salivary biomarkers' matrix metalloproteinase-8 (MMP-8) and myeloperoxidase (MPO) in patients with periodontitis. METHODS: A total of 120 participants aged 25-55 were categorized into three groups: MetS with periodontitis (n = 40); systemically healthy with periodontitis (n = 40); and systemically and periodontally healthy controls (n = 40). Data collected included systemic parameters like waist circumference (WC), blood pressure (BP), high- and low-density lipoproteins, triglycerides (TG), fasting blood sugar (FBS), and glycated hemoglobin (HbA1c). Periodontal parameters estimated included bleeding on probing score (BoP), full-mouth plaque score (FMPS), periodontal probing depth (PPD), clinical attachment loss (CAL), and the number of missing teeth. Unstimulated whole saliva was analyzed via ELISA for active MMP-8 (aMMP-8), total MMP-8 (tMMP-8), and MPO. RESULTS: Participants with MetS and periodontitis exhibited significantly higher periodontal parameters, salivary aMMP-8, and MPO (26.26 vs. 24.1 ng/mL and 13.53 vs. 11.55 ng/mL compared to systemically healthy periodontitis patients) (all p < 0.01). Positive correlations occurred between aMMP-8 and WC, TG, and FBS (p < 0.01), and between MPO and WC, BP, and TG (p < 0.01). CONCLUSIONS: The positive associations between these biomarkers and metabolic parameters indicate their potential utility for monitoring cardiovascular and glycemic risk in patients with periodontal disease.

"What's Next in My Arc of Development?": An Exploratory Study of What Medical Students Need to Care for Patients of Different Backgrounds.

PHENOMENON: Medical schools must equip future physicians to provide equitable patient care. The best approach, however, is mainly dependent on a medical school's context. Graduating students from our institution have reported feeling ill-equipped to care for patients from "different backgrounds" on the Association of American Medical Colleges' Graduation Questionnaire. We explored how medical students interpret "different patient backgrounds" and what they need to feel prepared to care for diverse patients. APPROACH: We conducted an exploratory qualitative case study using focus groups with 11, Year 2 (MS2) and Year 4 (MS4) medical students at our institution. Focus groups were recorded, transcribed, and coded using thematic analysis. We used Bobbie Harro's cycles of socialization and liberation to understand how the entire medical school experience, not solely the curriculum, informs how medical students learn to interact with all patients. FINDINGS: We organized our findings into four major themes to characterize students' medical education experience when learning to care for patients of different backgrounds: (1) Understandings of different backgrounds (prior to medical school); (2) Admissions process; (3) Curricular socialization; and (4) Co-curricular (or environmental) socialization. We further divided themes 2, 3, and 4 into two subthemes when learning how to care for patients of different backgrounds: (a) the current state and (b) proposed changes. We anticipate that following the proposed changes will help students feel more prepared to care for patients of differing backgrounds. INSIGHTS: Our findings show that preparing medical students to care for diverse patient populations requires a multitude of intentional changes throughout medical students' education. Using Harro's cycles of socialization and liberation as an analytic lens, we identified multiple places throughout medical students' educational experience that are barriers to learning how to care for diverse populations. We propose changes within medical students' education that build upon each other to adequately prepare students to care for patients of diverse backgrounds. Each proposed change culminates into a systemic shift within an academic institution and requires an intentional commitment by administration, faculty, admissions, curriculum, and student affairs.

Feasibility and Diagnostic Value of Recording Smartwatch Electrocardiograms in Neonates and Children.

OBJECTIVE: The objective of this study was to evaluate the agreement of smartwatch-derived single-lead electrocardiogram (ECG) recordings with 12-lead ECGs for diagnosing electrocardiographic abnormalities. STUDY DESIGN: A 12-lead ECG and an ECG using Apple Watch were obtained in 110 children (aged 1 week to 16 years) with normal (n = 75) or abnormal (n = 35) 12-lead ECGs (atrioventricular block [7], supraventricular tachycardia [SVT] {5}, bundle branch block [12], ventricular preexcitation [6], long QT [5]). In children aged <6 years, the ECG recording was performed with the active participation of an adult who applied the neonate or child's finger to the crown of the watch. In older children, tracings were obtained after brief teaching without adult guidance. All 12-lead ECGs were independently evaluated by 2 blinded cardiologists. Apple Watch ECGs were independently evaluated by another blinded cardiologist. RESULTS: In 109 children (99.1%), the smartwatch tracing was of sufficient quality for evaluation. Smartwatch tracings were 84% sensitive and 100% specific for the detection of an abnormal ECG. All 75 normal tracings were correctly identified. Of the 35 children with abnormalities on 12-lead ECGs, 5 (14%) were missed, most often because of baseline wander and artifacts. Rhythm disorders (atrioventricular block or SVT) and bundle branch blocks were correctly detected in most cases (11 of 12 and 11 of 12, respectively); preexcitation and long QT was detected in 4 of 6 and 4 of 5, respectively. CONCLUSION: Smartwatch ECGs recorded with parental assistance in children aged up to 6 years and independently in older children have the potential to detect clinically relevant conditions.

CONQUER Scleroderma: association of gastrointestinal tract symptoms in early disease with resource utilization.

OBJECTIVES: SSc is associated with increased health-care resource utilization and economic burden. The Collaborative National Quality and Efficacy Registry (CONQUER) is a US-based collaborative that collects longitudinal follow-up data on SSc patients with <5 years of disease duration enrolled at scleroderma centres in the USA. The objective of this study was to investigate the relationship between gastrointestinal tract symptoms and self-reported resource utilization in CONQUER participants. METHODS: CONQUER participants who had completed a baseline and 12-month Gastrointestinal Tract Questionnaire (GIT 2.0) and a Resource Utilization Questionnaire (RUQ) were included in this analysis. Patients were categorized by total GIT 2.0 severity: none-to-mild (0-0.49); moderate (0.50-1.00), and severe-to-very severe (1.01-3.00). Clinical features and medication exposures were examined in each of these categories. The 12-month RUQ responses were summarized by GIT 2.0 score categories at 12 months. RESULTS: Among the 211 CONQUER participants who met the inclusion criteria, most (64%) had mild GIT symptoms, 26% had moderate symptoms, and 10% severe GIT symptoms at 12 months. The categorization of GIT total severity score by RUQ showed that more upper endoscopy procedures and inpatient hospitalization occurred in the CONQUER participants with severe GIT symptoms. These patients with severe GIT symptoms also reported the use of more adaptive equipment. CONCLUSION: This report from the CONQUER cohort suggests that severe GIT symptoms result in more resource utilization. It is especially important to understand resource utilization in early disease cohorts when disease activity, rather than damage, primarily contributes to health-related costs of SSc.

Antenatal ultrasound features of isolated recurrent copy number variation in 7q11.23 (Williams syndrome and 7q11.23 duplication syndrome).

OBJECTIVE: We aimed to gather fetal cases carrying a 7q11.23 copy number variation (CNV) and collect precise clinical data to broaden knowledge of antenatal features in these syndromes. METHODS: We retrospectively recruited unrelated cases with 7q11.23 deletion, known as Williams-Beuren syndrome (WBS), or 7q11.23 duplication who had prenatal ultrasound findings. We collected laboratory and clinical data, fetal ultrasound, cardiac ultrasound and fetal autopsy reports from 18 prenatal diagnostic centers throughout France. RESULTS: 40 fetuses with WBS were collected and the most common features were intra-uterine growth retardation (IUGR) (70.0%, 28/40), cardiovascular defects (30.0%, 12/40), polyhydramnios (17.5%, 7/40) and protruding tongue (15.0%, 6/40). Fetal autopsy reports were available for 11 cases and were compared with ultrasound prenatal features. Four cases of fetuses with 7q11.23 microduplication were collected and prenatal ultrasound signs were variable and often isolated. CONCLUSION: This work strengthens the fact that 7q11.23 CNVs are associated with a broad spectrum of antenatal presentations. IUGR and cardiovascular defects were the most frequent ultrasound signs. By reporting the biggest series of antenatal WBS, we aim to better delineate distinctive signs in fetuses with 7q11.23 CNVs.

Expression of advanced glycation end products and their receptors in diabetic periodontitis patients.

AIM: The systematic review aimed to compare the levels of advanced glycation end products (AGEs) and RAGE (AGE receptors) expression in diabetic periodontitis patients with non-diabetic periodontitis patients and to identify the relationship of AGE and RAGE levels with periodontal disease severity. MATERIALS AND METHODS: The literature search was carried out according to PRISMA guidelines by two independent researchers using four online databases: PubMed, Scopus, Web of Science Core Collection, and Pro-Quest. Relevant studies published between 2000 and March 2023 were included in this review. The association of diabetes and AGE/RAGE levels on periodontal health, periodontal pocket depth (PPD), and clinical attachment loss (CAL) was studied. RESULTS: Sixteen cross-sectional studies, including 2794 patients (age range 15-75 years), were identified in the final stage. An elevated AGE level was observed among patients with diabetes and chronic periodontal disease compared to the non-diabetic group. Furthermore, the levels of AGE and RAGE are associated with CAL and PPD. Potential confounding factors like genetic and methodological differences were also responsible for AGE and RAGE variation. CONCLUSION: Levels of AGEs and RAGE expressions in diabetic periodontitis patients differ from non-diabetic periodontitis patients. The differences may impact the course and severity of periodontal disease.

High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness.

High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population.

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.

Using a smartwatch to record an electrocardiogram in the pediatric population.

The accuracy of smartwatch ECG recordings in adults has been demonstrated primarily in the automated diagnosis of atrial fibrillation. While the detection of atrial fibrillation is a priority among adults given the arrhythmia's prevalence and actionable ramifications, the potential value of smartwatch ECG recordings in children differs considerably. In this case series, we will describe some examples of smartwatch ECGs recorded in children, highlighting the feasibility and potential indications of this technology in the pediatric population.

Global Proteomic Profiling of Salmonella Infection by a Giant Phage.

The 240-kb Salmonella phage SPN3US genome encodes 264 gene products, many of which are functionally uncharacterized. We have previously used mass spectrometry to define the proteomes of wild-type and mutant forms of the SPN3US virion. In this study, we sought to determine whether this technique was suitable for the characterization of the SPN3US proteome during liquid infection. Mass spectrometry of SPN3US-infected cells identified 232 SPN3US and 1,994 Salmonella proteins. SPN3US proteins with related functions, such as proteins with roles in DNA replication, transcription, and virion formation, were coordinately expressed in a temporal manner. Mass spectral counts showed the four most abundant SPN3US proteins to be the major capsid protein, two head ejection proteins, and the functionally unassigned protein gp22. This high abundance of gp22 in infected bacteria contrasted with its absence from mature virions, suggesting that it might be the scaffold protein, an essential head morphogenesis protein yet to be identified in giant phages. We identified homologs to SPN3US gp22 in 45 related giant phages, including ϕKZ, whose counterpart is also abundant in infected bacteria but absent in the virion. We determined the ϕKZ counterpart to be cleaved in vitro by its prohead protease, an event that has been observed to promote head maturation of some other phages. Our findings are consistent with a scaffold protein assignment for SPN3US gp22, although direct evidence is required for its confirmation. These studies demonstrate the power of mass spectral analyses for facilitating the acquisition of new knowledge into the molecular events of viral infection.IMPORTANCE "Giant" phages with genomes >200 kb are being isolated in increasing numbers from a range of environments. With hosts such as Salmonella enterica, Pseudomonas aeruginosa, and Erwinia amylovora, these phages are of interest for phage therapy of multidrug-resistant pathogens. However, our understanding of how these complex phages interact with their hosts is impeded by the proportion (∼80%) of their gene products that are functionally uncharacterized. To develop the repertoire of techniques for analysis of phages, we analyzed a liquid infection of Salmonella phage SPN3US (240-kb genome) using third-generation mass spectrometry. We observed the temporal production of phage proteins whose genes collectively represent 96% of the SPN3US genome. These findings demonstrate the sensitivity of mass spectrometry for global proteomic profiling of virus-infected cells, and the identification of a candidate for a major head morphogenesis protein will facilitate further studies into giant phage head assembly.

RNA sequencing analysis of salt tolerance in soybean (Glycine max).

Salt stress causes foliar chlorosis and scorch, plant stunting, and eventually yield reduction in soybean. There are differential responses, namely tolerance (excluder) and intolerance (includer), among soybean germplasm. However, the genetic and physiological mechanisms for salt tolerance is complex and not clear yet. Based on the results from the screening of the RA-452 x Osage mapping population, two F4:6 lines with extreme responses, most tolerant and most sensitive, were selected for a time-course gene expression study in which the 250 mM NaCl treatment was initially imposed at the V1 stage and continued for 24 h (hrs). Total RNA was isolated from the leaves harvested at 0, 6, 12, 24 h after the initiation of salt treatment, respectively. The RNA-Seq analysis was conducted to compare the salt tolerant genotype with salt sensitive genotype at each time point using RNA-Seq pipeline method. A total of 2374, 998, 1746, and 630 differentially expressed genes (DEGs) between salt-tolerant line and salt-sensitive line, were found at 0, 6, 12, and 24 h, respectively. The expression patterns of 154 common DEGs among all the time points were investigated, of which, six common DEGs were upregulated and seven common DEGs were downregulated in salt-tolerant line. Moreover, 13 common DEGs were dramatically expressed at all the time points. Based on Log2 (fold change) of expression level of salt-tolerant line to salt-sensitive line and gene annotation, Glyma.02G228100, Glyma.03G226000, Glyma.03G031000, Glyma.03G031400, Glyma.04G180300, Glyma.04G180400, Glyma.05 g204600, Glyma.08G189600, Glyma.13G042200, and Glyma.17G173200, were considered to be the key potential genes involving in the salt-tolerance mechanism in the soybean salt-tolerant line.

Prevalence of Periodontal Disease among Obese Young Adult Population in Saudi Arabia-A Cross-Sectional Study.

Background and objectives: We aimed to assess the prevalence of periodontal disease among obese young adults in Saudi Arabia and to analyze the association between different body mass indexes and the severity of periodontal disease. Materials and methods: This descriptive cross-sectional study consisted of 307 obese patients aged 18-39 years, with body mass index (BMI) ≥30. Demographic variables for periodontal disease, anthropometric parameters such as BMI along with clinical parameters such as oral hygiene index-simplified, community periodontal index (CPI) score and loss of attachment (LOA), were assessed. Multivariate binary logistic regression analysis was used to identify the predictors for chronic periodontitis in obese young adults between 18-40 years of age. Results: The majority of the participants (71.3%) had periodontal disease. Obese and extremely obese patients together showed a statistically significant difference in the age group of 21-30 years in terms of CPI score for inflammation (p < 0.05) and LOA (p < 0.001). Logistic regression analysis showed age (OR: 3.180; 95%CL: 1.337-7.561; p <.001), occasional dental visit (OR: 5.965; 95%CL: 3.130-11.368; p < 0.001), smoking >10 cigarettes (OR: 11.868; 95%CL: 3.588-39.254; p < 0.001) and poor oral hygiene status (OR: 17.250; 95%CL: 6.958-42.764; p < 0.001) were associated with a significantly higher risk of having periodontal disease. Conclusions: This study showed a high prevalence of periodontal disease in obese patients among the Saudi Arabian population.

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly.

Giant tailed bacterial viruses, or phages, such as Pseudomonas aeruginosa phage ϕKZ, have long genomes packaged into large, atypical virions. Many aspects of ϕKZ and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. We hypothesized that the Salmonella enterica phage SPN3US could be a useful model phage to address this gap in knowledge. The 240-kb SPN3US genome shares a core set of 91 genes with ϕKZ and related phages, ∼61 of which are virion genes, consistent with the expectation that virion complexity is an ancient, conserved feature. Nucleotide sequencing of 18 mutants enabled assignment of 13 genes as essential, information which could not have been determined by sequence-based searches for 11 genes. Proteome analyses of two SPN3US virion protein mutants with knockouts in 64 and 241 provided new insight into the composition and assembly of giant phage heads. The 64 mutant analyses revealed all the genetic determinants required for assembly of the SPN3US head and a likely head-tail joining role for gp64, and its homologs in related phages, due to the tailless-particle phenotype produced. Analyses of the mutation in 241, which encodes an RNA polymerase ß subunit, revealed that without this subunit, no other subunits are assembled into the head, and enabled identification of a "missing" ß' subunit domain. These findings support SPN3US as an excellent model for giant phage research, laying the groundwork for future analyses of their highly unusual virions, host interactions, and evolution. IMPORTANCE: In recent years, there has been a paradigm shift in virology with the realization that extremely large viruses infecting prokaryotes (giant phages) can be found in many environments. A group of phages related to the prototype giant phage ϕKZ are of great interest due to their virions being among the most complex of prokaryotic viruses and their potential for biocontrol and phage therapy applications. Our understanding of the biology of these phages is limited, as a large proportion of their proteins have not been characterized and/or have been deemed putative without any experimental verification. In this study, we analyzed Salmonella phage SPN3US using a combination of genomics, genetics, and proteomics and in doing so revealed new information regarding giant phage head structure and assembly and virion RNA polymerase composition. Our findings demonstrate the suitability of SPN3US as a model phage for the growing group of phages related to ϕKZ.

Head-to-head comparison between 18F-FDOPA PET/CT and MR/CT angiography in clinically recurrent head and neck paragangliomas.

PURPOSE: Head and neck paragangliomas (HNPGLs) can relapse after primary treatment. Optimal imaging protocols have not yet been established for posttreatment evaluation. The aim of the present study was to assess the diagnostic value of 18F-FDOPA PET/CT and MR/CT angiography (MRA/CTA) in HNPGL patients with clinical relapse during their follow-up. METHODS: Sixteen consecutive patients presenting with local pain, tinnitus, dysphagia, hoarse voice, cranial nerve involvement, deafness, or retrotympanic mass appearing during follow-up after the initial treatment of HNPGLs were retrospectively evaluated. Patients underwent both 18F-FDOPA PET/CT and MRA (15 patents) or CTA (1 patent). Both methods were first assessed under blinded conditions and afterwards correlated. Head and neck imaging abnormalities without histological confirmation were considered true-positive results based on a consensus between radiologists and nuclear physicians and on further 18F-FDOPA PET/CT and/or MRA. RESULTS: 18F-FDOPA PET/CT and MRA/CTA were concordant in 14 patients and in disagreement in 2 patients. 18F-FDOPA PET/CT and MRA/CTA identified, respectively, 12 and 10 presumed recurrent HNPGLs in 12 patients. The two lesions diagnosed by PET/CT only were confirmed during follow-up by otoscopic examination and MRA performed 29 and 17 months later. 18F-FDOPA PET/CT images were only slightly influenced by the posttreatment sequelae, showing a better interobserver reproducibility than MRA/CTA. Finally, in 2 of the 16 studied patients, 18F-FDOPA PET/CT detected two additional synchronous primary HNPGLs. CONCLUSION: 18F-FDOPA PET/CT is highly sensitive in posttreatment evaluation of patients with HNPGLs, and also offers better interobserver reproducibility than MRA/CTA and whole-body examination. We therefore suggest that 18F-FDOPA PET/CT is performed as the first diagnostic imaging modality in symptomatic patients with suspicion of HNPGL relapse after primary treatment when 68Ga-labeled somatostatin analogues are not available.

[Development of valorization of physical activity: the role of HIV associations]. / La construction de la valorisation de l'activité physique : le rôle des associations VIH.

With the arrival of triple combination therapy in 1996-1997, HIV infection, considered up until then to be a life-threatening condition, changed statuses within the realm of public health actions Progressively likened to a "chronic illness", the discourse on HIV prevention targeting people living with HIV (PLHIV) began to evolve. A review of the scientific literature and the journals of four national HIV associations published between 1990 and 2010 shows that physical activities, previously discouraged because considered to be dangerous, have become increasingly presented as a means of improving quality of life and are increasingly recommended for PLHIV. This article studies this reconfiguration of the discourse on HIV prevention, as well as its effects on the discourse conveyed by HIV associations. The article shows how the new classification of HIV as a "chronic illness", on the basis of scientific expertise, has led to a modified discourse on prevention, including the recommendation of regular and controlled physical activity. This new orientation has contributed to the restructuring of HIV associations which relay this discourse and modify their organization and services, increasingly offering access to physical activities. However, this raises the question of the effects of this new representation of physical activities, as there has been little conside-ration of the difficulties encountered by PLHIV to respond to these repeated encouragements to modify their lifestyles in order to be "good" chronically ill patients. .

The Maize TFome--development of a transcription factor open reading frame collection for functional genomics.

Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/).

Early versus late preemptive allogeneic hematopoietic cell transplantation for relapsed or refractory acute myeloid leukemia.

Many patients with relapsed or refractory acute myeloid leukemia (AML) do not receive allogeneic hematopoietic cell transplantation (alloHCT) because they are unable to achieve a complete remission (CR) after reinduction chemotherapy. Starting in January 2003, we prospectively assigned patients with AML with high-risk clinical features to preemptive alloHCT (p-alloHCT) as soon as possible after reinduction chemotherapy. High-risk clinical features were associated with poor response to chemotherapy: primary induction failure, second or greater relapse, and first CR interval <6 months. We hypothesized that any residual disease would be maximally reduced at the time of transplant, resulting in the best milieu and most lead time for developing a graft-versus-leukemia effect and in improved long-term overall survival (OS) without excess toxicity. This analysis studied the effect of transplant timing on p-alloHCT in 30 patients with high-risk clinical features of 156 consecutive AML patients referred for alloHCT. We compared early p-alloHCT within 4 weeks of reinduction chemotherapy before count recovery with late p-alloHCT 4 weeks after reinduction chemotherapy with count recovery. OS and progression-free survival (PFS) at 2 years were not significantly different for early versus late p-alloHCT (OS 23% versus 33%, respectively, P > .1; PFS 18% versus 22%, respectively, P > .1). Day 100 and 1-year transplant-related mortality were similar (33.3% versus 22.2%, P > .1; 44.4% versus 42.9%, P > .1, respectively). Preemptive alloHCT allowed 30 patients to be transplanted who would normally not receive alloHCT. Clinical outcomes for early p-alloHCT are similar to those for late p-alloHCT without excess toxicity. Early p-alloHCT is a feasible alternative to late p-alloHCT for maximizing therapy of AML that is poorly responsive to induction chemotherapy.

Mutational analysis of the Pseudomonas aeruginosa myovirus KZ morphogenetic protease gp175.

Pseudomonas aeruginosa myovirus KZ has a 270-kb genome within a T=27 icosahedral capsid that contains a large, unusual, and structurally well-defined protein cylindrical inner body (IB) spanning its interior. Proteolysis forms a pivotal stage in KZ head and IB morphogenesis, with the protease gp175 cleaving at least 19 of 49 different head proteins, including the major capsid protein and five major structural IB proteins. Here we show that the purified mature form of gp175 is active and cleaves purified IB structural proteins gp93 and gp89. Expression vector synthesis and purification of the zymogen/precursor yielded an active, mature-length protease, showing independent C-terminal gp175 self-cleavage autoactivation. Mutation of either the predicted catalytic serine or histidine inactivated mature gp175, supporting its classification as a serine protease and representing the first such direct biochemical demonstration with purified protease and substrate proteins for any phage protease. These mutations also blocked self-cleavage of the precursor while allowing intermolecular gp175 processing. To confirm the cleavage specificity of gp175, we mutated three cleavage sites in gp93, which blocked proteolysis at these sites. The N-terminal propeptide of gp93 was shown to undergo more extensive proteolysis than previously identified. We found that proteolysis in gp93 progressed from the N to C terminus, while blocking cleavage sites slowed but did not eliminate downstream proteolysis. These findings were shown by informatics to be relevant to the head morphogenesis of numbers of other related IB-containing giant phages as well as to T4 and herpesviruses, which have homologous proteases.

Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches.

In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.

Assessment of the Nonlinear Electrophoretic Migration of Nanoparticles and Bacteriophages.

Bacteriophage therapy presents a promising avenue for combating antibiotic-resistant bacterial infections. Yet, challenges exist, particularly, the lack of a straightforward purification pipeline suitable for widespread application to many phage types, as some phages are known to undergo significant titer loss when purified via current techniques. Electrokinetic methods offer a potential solution to this hurdle, with nonlinear electrophoresis emerging as a particularly appealing approach due to its ability to discern both the size and shape of the target phage particles. Presented herein is the electrokinetic characterization of the mobility of nonlinear electrophoresis for two phages (SPN3US and ϕKZ) and three types of polystyrene nanoparticles. The latter served as controls and were selected based on their sizes and surface charge magnitude. Particle tracking velocimetry experiments were conducted to characterize the mobility of all five particles included in this study. The results indicated that the selected nanoparticles effectively replicate the migration behavior of the two phages under electric fields. Further, it was found that there is a significant difference in the nonlinear electrophoretic response of phages and that of host cells, as first characterized in a previous report, illustrating that electrokinetic-based separations are feasible. The findings from this work are the first characterization of the behavior of phages under nonlinear electrophoresis effects and illustrate the potential for the development of electrokinetic-based phage purification techniques that could aid the advancement of bacteriophage therapy.