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Trait prioritization studies have guided research, development and investment decisions for public-sector crop breeding programmes since the 1970s, but the research design, methods and tools underpinning these studies are not well understood. We used PRISMA-ScR (Preferred Reporting Items for Systematic review and Meta-Analysis Protocols) to evaluate research on trait ranking for major crops over the past 40 years (1980-2023). Data extraction and descriptive analysis on 657 papers show uneven attention to crops, lack of systematic sex disaggregation and regional bias. The lack of standardized trait data taxonomy across studies, and inconsistent research design and data collection practices make cross-comparison of findings impossible. In addition, network mapping of authors and donors shows patterns of concentration and the presence of silos within research areas. This study contributes to the next generation of innovation in trait preference studies to produce more inclusive, demand-driven varietal design that moves beyond trait prioritization focused on productivity and yield.
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Productos Agrícolas , Fitomejoramiento , Productos Agrícolas/genética , Productos Agrícolas/crecimiento & desarrollo , Fitomejoramiento/métodosRESUMEN
BACKGROUND: One in four people experience a mental health problem every year and improving mental health care is an international priority. In the course of their work, pharmacists frequently encounter people with mental health problems. The experience of mental health teaching, including Mental Health First Aid (MHFA) training, in undergraduate pharmacy (MPharm) students in the UK and Ireland is not well documented. Students' viewpoints, contextualised with curricular overviews provided by staff, were analysed to understand their experience. METHODS: An anonymous, online questionnaire was distributed to MPharm students and staff in the UK and Ireland. Students were asked closed questions regarding their course and exposure to MHFA, which were analysed using descriptive statistics. Open questions were included to enable explanations and these data were used to contextualise the quantitative findings. One member of staff from each university was invited to answer a modified staff version of the questionnaire, to provide a curriculum overview and staff perspective. RESULTS: 232 students and 13 staff, from 22 universities, responded. Three-quarters of students did not agree with the statement that 'mental health was embedded throughout the MPharm'. Most students (80.6%) stated that they were taught neuropharmacology whilst 44.8% stated that their course included communicating with people about their mental health. One-third (33.2%) of students stated that their degree 'adequately prepared them to help people with their mental health'. Twenty-six students (11.6%) had completed MHFA training of which 89% would endorse inclusion of this within the MPharm. Of those who had not completed the training, 81% expressed a desire to do so. Those who completed MHFA training self-reported greater preparedness than those who did not, but student numbers were small. CONCLUSIONS: Mental health teaching for pharmacy undergraduates is more focussed on theoretical aspects rather than applied skills. MHFA was viewed by students as one way to enhance skill application. The association of the increased self-reported preparedness of those who completed MHFA could be confounded by a positive environmental cultural. MPharm programmes need sufficient focus on real-world skills such as communication and crisis response, to complement the fundamental science.
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STUDY QUESTION: Does a single oral dose of nolasiban 900 mg administered 4 h before embryo transfer (ET) increase pregnancy rates in women undergoing IVF? SUMMARY ANSWER: In an individual patient data (IPD) meta-analysis of three clinical trials, a single oral dose of nolasiban 900 mg was associated with an increased ongoing pregnancy rate of an absolute 5% (relative 15%). WHAT IS KNOWN ALREADY: Several clinical studies have shown that blocking activation of oxytocin receptors by an oxytocin receptor (OTR) antagonist has the potential to decrease uterine contractions, increase endometrial perfusion and enhance endometrial decidualisation and other parameters of endometrial receptivity. It has been hypothesised that antagonism of oxytocin receptors could improve the likelihood of successful embryo implantation and thus increase pregnancy and live birth rates following ET. STUDY DESIGN, SIZE, DURATION: This is an analysis of three randomised, double-blind, placebo-controlled trials, which randomised 1836 subjects between 2015 and 2019. We describe the results of a meta-analysis of individual participant data (IPD) from all three trials and the pre-specified analyses of each individual trial. PARTICIPANT/MATERIAL, SETTING, METHODS: Participants were patients undergoing ET following IVF/ICSI in 60 fertility centres in 11 European countries. Study subjects were below 38 years old and had no more than one previously failed cycle. They were randomised to a single oral dose of nolasiban 900 mg (n = 846) or placebo (n = 864). In IMPLANT 1, additional participants were also randomised to nolasiban 100 mg (n = 62) or 300 mg (n = 60). Fresh ET of one good quality embryo (except in IMPLANT 1 where transfer of two embryos was allowed) was performed on Day 3 or Day 5 after oocyte retrieval, approximately 4 h after receiving the study treatment. Serum hCG levels were collected at 14 days post oocyte retrieval (Week 2) and for women with a positive hCG result, ultrasound was performed at Week 6 post-ET (clinical pregnancy) and at Week 10 post-ET (ongoing pregnancy). Pregnant patients were followed for maternal (adverse events), obstetric (live birth, gestational age at delivery, type of delivery, incidence of twins) and neonatal (sex, weight, height, head circumference, Apgar scores, congenital anomalies, breast feeding, admission to intensive care and specific morbidities e.g. jaundice, respiratory distress syndrome) outcomes. MAIN RESULTS AND THE ROLE OF CHANCE: In an IPD meta-analysis of the clinical trials, a single oral dose of nolasiban 900 mg was associated with an absolute increase of 5.0% (95% CI 0.5, 9.6) in ongoing pregnancy rate and a corresponding increase of 4.4% (95% CI -0.10, 8.93) in live birth rate compared to placebo. Similar magnitude increases were observed for D3 or D5 transfers but were not significantly different from the placebo. Population pharmacokinetics (PK) demonstrated a correlation between higher exposures and pregnancy. LIMITATIONS, REASON FOR CAUTION: The meta-analysis was not a pre-specified analysis. While the individual trials did not show a consistent significant effect, they were not powered based on an absolute increase of 5% in ongoing pregnancy rate. Only a single dose of up to 900 mg nolasiban was administered in the clinical trials; higher doses or extended regimens have not been tested. Only fresh ET has been assessed in the clinical trials to date. WIDER IMPLICATIONS OF THE FINDINGS: The finding support the hypothesis that oxytocin receptor antagonism at the time of ET can increase pregnancy rates following IVF. The overall clinical and population PK data support future evaluation of higher doses and/or alternate regimens of nolasiban in women undergoing ET following IVF. STUDY FUNDING/COMPETING INTERESTS: The trials were designed, conducted and funded by ObsEva SA. A.H., O.P., E.G., E.L. are employees and stockholders of ObsEva SA. E.L. is a board member of ObsEva SA. G.G. reports honoraria and/or non-financial support from ObsEva, Merck, MSD, Ferring, Abbott, Gedeon-Richter, Theramex, Guerbet, Finox, Biosilu, Preglem and ReprodWissen GmbH. C.B. reports grants and honoraria from ObsEva, Ferring, Abbott, Gedeon Richter and MSD. P.P. reports consulting fees from ObsEva. H.T. reports grants and or fees from ObsEva, Research Fund of Flanders, Cook, MSD, Roche, Gedeon Richter, Abbott, Theramex and Ferring. H.V. reports grants from ObsEva and non-financial support from Ferring. P.T. is an employee of Cytel Inc., who provides statistical services to ObsEva. J.D. reports consulting fees and other payments from ObsEva and, Scientific Advisory Board membership of ObsEva. TRIAL REGISTRATION NUMBERS: ClinicalTrials.gov: NCT02310802, NCT03081208, NCT03758885. TRIAL REGISTRATION DATES: December 2014 (NCT02310802), March 2017 (NCT03081208), November 2018 (NCT03758885). FIRST PATIENT'S ENROLMENT: January 2015 (NCT02310802), March 2017 (NCT03081208), November 2018 (NCT03758885).
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Receptores de Oxitocina , Inyecciones de Esperma Intracitoplasmáticas , Adulto , Transferencia de Embrión , Europa (Continente) , Femenino , Fertilización In Vitro , Humanos , Recién Nacido , Oximas , Oxitocina , Embarazo , Índice de Embarazo , Pirrolidinas , Ensayos Clínicos Controlados Aleatorios como AsuntoRESUMEN
STUDY DESIGN: In 2014, the adult spinal cord injury (SCI) common data element (CDE) recommendations were made available. This project was a review of the adult SCI CDE for relevance to children and youth with SCI. OBJECTIVES: The objective of this study was to review the National Institute of Neurologic Disorders and Stroke (NINDS) adult SCI CDEs for relevance to children and youth with SCI. SETTING: International. METHODS: The pediatric working group consisted of international members with varied fields of expertise related to pediatric SCI. The group convened biweekly meetings for 6 months in 2015. All of the adult SCI CDEs were reviewed, evaluated and modified/created for four age groups: 0-5 years, 6-12 years, 13-15 years and 16-18 years. Whenever possible, results of published research studies were used to guide recommendations. In the absence of empirical support, grey literature and international content expert consensus were garnered. Existing pediatric NINDS CDEs and new CDEs were developed in areas where adult recommendations were not appropriate. After internal working group review of domain recommendations, these pediatric CDEs were vetted during a public review from November through December 2015. RESULTS: Version 1.0 of the pediatric SCI CDEs was posted in February 2016. CONCLUSION: The pediatric SCI CDEs are incorporated directly into the NINDS SCI CDE sets and can be found at https://commondataelements.ninds.nih.gov.
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Elementos de Datos Comunes , Traumatismos de la Médula Espinal , Adolescente , Niño , Preescolar , Humanos , Lactante , Recién Nacido , National Institute of Neurological Disorders and Stroke (U.S.) , Traumatismos de la Médula Espinal/diagnóstico , Traumatismos de la Médula Espinal/epidemiología , Traumatismos de la Médula Espinal/terapia , Estados UnidosRESUMEN
AIMS: To determine whether poultry litter marker gene LA35 is correlated with pathogens and fecal indicator bacteria (FIB) in run-off from poultry litter-amended plots. METHODS AND RESULTS: A rainfall simulator with various vegetative filter strip lengths was employed to evaluate the correlation of a microbial source tracking (MST) marker for poultry feces/litter (the 16S rRNA gene of Brevibacterium sp. LA35 [LA35] measured by quantitative PCR) with pathogens and FIB in run-off. LA35 was correlated with Staphylococcus aureus, Escherichia coli, Enterococcus spp. and Bacteroidales levels. Salmonella was present at low concentration in litter, but became undetectable by qPCR in run-off. Escherichia coli, LA35 and Staph. aureus exhibited mass-based first flush behaviour in the run-off. CONCLUSIONS: Correlation of LA35 with FIB and pathogens in run-off from poultry litter-amended fields suggest comparable transport mechanisms and that LA35 is a useful tracer for harmful bacteria in the environment released from poultry litter. SIGNIFICANCE AND IMPACT OF THE STUDY: To protect human health, an effective marker for poultry fecal contamination should exhibit similar fate and transport characteristics compared to pathogens. This study is among the first to demonstrate such a relationship in run-off for a MST marker.
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Bacterias/aislamiento & purificación , Genes Bacterianos , Aves de Corral/microbiología , Animales , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Brevibacterium/genética , Brevibacterium/aislamiento & purificación , Enterococcus/genética , Enterococcus/aislamiento & purificación , Escherichia coli/genética , Escherichia coli/aislamiento & purificación , Heces/microbiología , Marcadores Genéticos , ARN Ribosómico 16S/genética , Lluvia , Salmonella/genética , Salmonella/aislamiento & purificación , Microbiología del Suelo , Staphylococcus aureus/genética , Staphylococcus aureus/aislamiento & purificación , Microbiología del AguaRESUMEN
OBJECTIVE: To develop an understanding of the stability of mental health during imprisonment through review of existing research evidence relating physical prison environment to mental state changes in prisoners. METHOD: A systematic literature search was conducted looking at changes in mental state and how this related to various aspects of imprisonment and the prison environment. RESULTS: Fifteen longitudinal studies were found, and from these, three broad themes were delineated: being imprisoned and aspects of the prison regime; stage of imprisonment and duration of sentence; and social density. Reception into prison results in higher levels of psychiatric symptoms that seem to improve over time; otherwise, duration of imprisonment appears to have no significant impact on mental health. Regardless of social density, larger prisons are associated with poorer mental state, as are extremes of social density. CONCLUSION: There are large gaps in the literature relating prison environments to changes in mental state; in particular, high-quality longitudinal studies are needed. Existing research suggests that although entry to prison may be associated with deterioration in mental state, it tends to improve with time. Furthermore, overcrowding, ever more likely as prison populations rise, is likely to place a particular burden on mental health services.
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Trastornos Mentales/psicología , Prisioneros/psicología , Medio Social , HumanosRESUMEN
BACKGROUND: Enzyme-linked immunoassays of full-length (M65) and/or caspase-cleaved (M30) cytokeratin 18 (CK18) released from epithelial cells undergoing necrosis and/or apoptosis, respectively, may have prognostic or predictive biomarker utility in a range of solid tumour types. Characterisation of baseline levels of circulating full length and cleaved CK18 specifically in patients with pancreatic cancer. METHODS: Plasma samples from 103 patients with pancreatic cancer stored at -80 degrees C were assayed for M65 and M30 levels. The median (inter-quartile range (IQR)) duration of plasma storage was 34 (23-57) months. Patients with metastatic disease (n=19) were found to have greater median (IQR) M65 levels (1145 (739-1698) U l(-1)) compared with the locally advanced (n=20; 748 (406-1150) U l(-1)) and resected (n=64; 612 (331-987) U l(-1)) patients (P=0.002). Elevated M65 levels were associated with poorer overall survival on univariate (P<0.001) but not multivariate (P=0.202) analysis. M65 concentrations also exhibited significant associations with concurrent serum-bilirubin levels (P<0.001) and the duration of plasma storage (P<0.001). CONCLUSIONS: Baseline plasma CK18 levels in pancreatic cancer are affected by the presence of obstructive jaundice and prolonged plasma storage. Clinical biomarker studies utilising serial CK18 levels are warranted in pancreatic cancer, provided consideration is given to these potentially confounding factors.
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Biomarcadores de Tumor/sangre , Queratina-18/sangre , Neoplasias Pancreáticas/diagnóstico , Anciano , Apoptosis , Antígeno CA-19-9/sangre , Ensayo de Inmunoadsorción Enzimática , Femenino , Humanos , Masculino , Persona de Mediana Edad , Necrosis , Neoplasias Pancreáticas/sangre , Neoplasias Pancreáticas/mortalidadRESUMEN
Clusterin is a heterodimeric glycoprotein found in many tissues of the body and is the most abundant protein secreted by cultured rat Sertoli cells. The function of clusterin is unknown, but it has been associated with cellular injury, lipid transport, apoptosis, and it may be involved in the clearance of cellular debris caused by cell injury or death. Consistent with this last idea, clusterin has been shown to bind to a variety of molecules with high affinity including lipids, peptides, and proteins and the hydrophobic probe 1-anilino-8-naphthalenesulfonate (ANS). Given this variety of ligands, clusterin must have specific structural features that provide the protein with its promiscuous binding activity. Using sequence analyses, we show that clusterin likely contains three long regions of natively disordered or molten globule-like structures containing putative amphipathic alpha-helices. These disordered regions were highly sensitive to trypsin digestion, indicating a flexible nature. The effects of denaturation on the fluorescence of the clusterin-ANS complex were compared between proteins with structured binding pockets and molten globular forms of proteins. Clusterin bound ANS in a manner that was very similar to that of molten globular proteins. Furthermore, we found that, when bound to ANS, at least one cleavage site within the protease-sensitive disordered regions of clusterin was protected from trypsin digestion. In addition, we show that clusterin can function as a biological detergent that can solubilize bacteriorhodopsin. We propose that natively disordered regions with amphipathic helices form a dynamic, molten globule-like binding site and provide clusterin the ability to bind to a variety of molecules.
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Glicoproteínas/metabolismo , Chaperonas Moleculares/metabolismo , Secuencia de Aminoácidos , Animales , Bacteriorodopsinas/metabolismo , Células Cultivadas , Dicroismo Circular , Clusterina , Glicoproteínas/química , Humanos , Hidrólisis , Masculino , Chaperonas Moleculares/química , Datos de Secuencia Molecular , Unión Proteica , Estructura Secundaria de Proteína , Ratas , Células de SertoliRESUMEN
The DNA-repair protein XPA is required to recognize a wide variety of bulky lesions during nucleotide excision repair. Independent NMR solution structures of a human XPA fragment comprising approximately 40% of the full-length protein, the minimal DNA-binding domain, revealed that one-third of this molecule was disordered. To better characterize structural features of full-length XPA, we performed time-resolved trypsin proteolysis on active recombinant Xenopus XPA (xXPA). The resulting proteolytic fragments were analyzed by electrospray ionization interface coupled to a Fourier transform ion cyclotron resonance mass spectrometry and SDS-PAGE. The molecular weight of the full-length xXPA determined by mass spectrometry (30922.02 daltons) was consistent with that calculated from the sequence (30922.45 daltons). Moreover, the mass spectrometric data allowed the assignment of multiple xXPA fragments not resolvable by SDS-PAGE. The neural network program Predictor of Natural Disordered Regions (PONDR) applied to xXPA predicted extended disordered N- and C-terminal regions with an ordered internal core. This prediction agreed with our partial proteolysis results, thereby indicating that disorder in XPA shares sequence features with other well-characterized intrinsically unstructured proteins. Trypsin cleavages at 30 of the possible 48 sites were detected and no cleavage was observed in an internal region (Q85-I179) despite 14 possible cut sites. For the full-length xXPA, there was strong agreement among PONDR, partial proteolysis data, and the NMR structure for the corresponding XPA fragment.
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Reparación del ADN/fisiología , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/fisiología , Secuencias de Aminoácidos/genética , Secuencias de Aminoácidos/fisiología , Secuencia de Aminoácidos , Animales , Electroforesis en Gel de Poliacrilamida , Hidrólisis , Redes Neurales de la Computación , Estructura Secundaria de Proteína , Espectrometría de Masa por Ionización de Electrospray , Espectroscopía Infrarroja por Transformada de Fourier , Tripsina , Xenopus laevis , Proteína de la Xerodermia Pigmentosa del Grupo ARESUMEN
Proteins can exist in a trinity of structures: the ordered state, the molten globule, and the random coil. The five following examples suggest that native protein structure can correspond to any of the three states (not just the ordered state) and that protein function can arise from any of the three states and their transitions. (1) In a process that likely mimics infection, fd phage converts from the ordered into the disordered molten globular state. (2) Nucleosome hyperacetylation is crucial to DNA replication and transcription; this chemical modification greatly increases the net negative charge of the nucleosome core particle. We propose that the increased charge imbalance promotes its conversion to a much less rigid form. (3) Clusterin contains an ordered domain and also a native molten globular region. The molten globular domain likely functions as a proteinaceous detergent for cell remodeling and removal of apoptotic debris. (4) In a critical signaling event, a helix in calcineurin becomes bound and surrounded by calmodulin, thereby turning on calcineurin's serine/threonine phosphatase activity. Locating the calcineurin helix within a region of disorder is essential for enabling calmodulin to surround its target upon binding. (5) Calsequestrin regulates calcium levels in the sarcoplasmic reticulum by binding approximately 50 ions/molecule. Disordered polyanion tails at the carboxy terminus bind many of these calcium ions, perhaps without adopting a unique structure. In addition to these examples, we will discuss 16 more proteins with native disorder. These disordered regions include molecular recognition domains, protein folding inhibitors, flexible linkers, entropic springs, entropic clocks, and entropic bristles. Motivated by such examples of intrinsic disorder, we are studying the relationships between amino acid sequence and order/disorder, and from this information we are predicting intrinsic order/disorder from amino acid sequence. The sequence-structure relationships indicate that disorder is an encoded property, and the predictions strongly suggest that proteins in nature are much richer in intrinsic disorder than are those in the Protein Data Bank. Recent predictions on 29 genomes indicate that proteins from eucaryotes apparently have more intrinsic disorder than those from either bacteria or archaea, with typically > 30% of eucaryotic proteins having disordered regions of length > or = 50 consecutive residues.
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Conformación Proteica , Proteínas/química , Proteínas/fisiología , Modelos Moleculares , Pliegue de Proteína , Estructura Terciaria de Proteína , Proteínas/genética , Relación Estructura-ActividadRESUMEN
To investigate the determinants of protein order and disorder, three primary and one derivative database of intrinsically disordered proteins were compiled. The segments in each primary database were characterized by one of the following: X-ray crystallography, nuclear magnetic resonance (NMR), or circular dichroism (CD). The derivative database was based on homology. The three primary disordered databases have a combined total of 157 proteins or segments of length.30 with 18,010 residues, while the derivative database contains 572 proteins from 32 families with 52,688 putatively disordered residues. For the four disordered databases, the amino acid compositions were compared with those from a database of ordered structure. Relative to the ordered protein, the intrinsically disordered segments in all four databases were significantly depleted in W, C, F, I, Y, V, L and N, significantly enriched in A, R, G, Q, S, P, E and K, and inconsistently different in H, M, T, and D, suggesting that the first set be called order-promoting and the second set disorder-promoting. Also, 265 amino acid properties were ranked by their ability to discriminate order and disorder and then pruned to remove the most highly correlated pairs. The 10 highest-ranking properties after pruning consisted of 2 residue contact scales, 4 hydrophobicity scales, 3 scales associated with.-sheets and one polarity scale. Using these 10 properties for comparisons of the 3 primary databases suggests that disorder in all 3 databases is very similar, but with those characterized by NMR and CD being the most similar, those by CD and X-ray being next, and those by NMR and X-ray being the least similar.
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Aminoácidos/química , Proteínas/química , Aminoácidos/análisis , Dicroismo Circular , Cristalografía por Rayos X , Interpretación Estadística de Datos , Bases de Datos Factuales , Pliegue de ProteínaRESUMEN
Intrinsic disorder refers to segments or to whole proteins that fail to self-fold into fixed 3D structure, with such disorder sometimes existing in the native state. Here we report data on the relationships among intrinsic disorder, sequence complexity as measured by Shannon's entropy, and amino acid composition. Intrinsic disorder identified in protein crystal structures, and by nuclear magnetic resonance, circular dichroism, and prediction from amino acid sequence, all exhibit similar complexity distributions that are shifted to lower values compared to, but significantly overlapping with, the distribution for ordered proteins. Compared to sequences from ordered proteins, these variously characterized intrinsically disordered segments and proteins, and also a collection of low-complexity sequences, typically have obviously higher levels of protein-specific subsets of the following amino acids: R, K, E, P, and S, and lower levels of subsets of the following: C, W, Y, I, and V. The Swiss Protein database of sequences exhibits significantly higher amounts of both low-complexity and predicted-to-be-disordered segments as compared to a non-redundant set of sequences from the Protein Data Bank, providing additional data that nature is richer in disordered and low-complexity segments compared to the commonness of these features in the set of structurally characterized proteins.
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Proteínas/química , Inteligencia Artificial , Secuencia de Bases , Bases de Datos Factuales , Modelos Moleculares , Desnaturalización Proteica , Pliegue de Proteína , Estructura Terciaria de Proteína , TermodinámicaRESUMEN
Viscoelastic properties of wet and dry human compact bone were studied in torsion and in bending for both the longitudinal and transverse directions at frequencies from 5 mHz to 5 kHz in bending to more than 50 kHz in torsion. Two series of tests were done for different longitudinal and transverse specimens from a human tibia. Wet bone exhibited a larger viscoelastic damping tan delta (phase between stress and strain sinusoids) than dry bone over a broad range of frequency. All the results had in common a relative minimum in tan delta over a frequency range, 1 to 100 Hz, which is predominantly contained in normal activities. This behavior is inconsistent with an optimal "design" for bone as a shock absorber. There was no definitive damping peak in the range of frequencies explored, which could be attributed to fluid flow in the porosity of bone.
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Huesos/fisiología , Anciano , Ingeniería Biomédica/instrumentación , Líquidos Corporales/fisiología , Huesos/anatomía & histología , Elasticidad , Humanos , Técnicas In Vitro , Masculino , Modelos Biológicos , ViscosidadRESUMEN
Petunia (Petunia hybrida) pollen requires flavonols (Fl) to germinate. Adding kaempferol to Fl-deficient pollen causes rapid and synchronous germination and tube outgrowth. We exploited this system to identify genes responsive to Fls and to examine the changes in gene expression that occur during the first 0.5 h of pollen germination. We used a subtracted library and differential screening to identify 22 petunia germinating pollen clones. All but two were expressed exclusively in pollen and half of the clones were rare or low abundance cDNAs. RNA gel-blot analysis showed that the steady-state transcript levels of all the clones were increased in response to kaempferol. The sequences showing the greatest response to kaempferol encode proteins that have regulatory or signaling functions and include S/D4, a leucine-rich repeat protein, S/D1, a LIM-domain protein, and D14, a putative Zn finger protein with a heme-binding site. Eight of the clones were novel including S/D10, a cDNA only expressed very late in pollen development and highly up-regulated during the first 0.5 h of germination. The translation product of the S/D3 cDNA shares some features with a neuropeptide that regulates guidance and growth in the tips of extending axons. This study confirmed that the bulk of pollen mRNA accumulates well before germination, but that specific sequences are transcribed during the earliest moments of Fl-induced pollen germination.
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Flavonoides , Germinación/efectos de los fármacos , Quempferoles , Proteínas de Plantas/genética , Polen/fisiología , Quercetina/análogos & derivados , Solanaceae/genética , Secuencia de Aminoácidos , Clonación Molecular , ADN Complementario , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Datos de Secuencia Molecular , Unión Proteica , Quercetina/farmacología , ARN Mensajero/genética , Secuencias Repetitivas de Aminoácido , Solanaceae/fisiologíaRESUMEN
Intrinsic protein disorder refers to segments or to whole proteins that fail to fold completely on their own. Here we predicted disorder on protein sequences from 34 genomes, including 22 bacteria, 7 archaea, and 5 eucaryotes. Predicted disordered segments > or = 50, > or = 40, and > or = 30 in length were determined as well as proteins estimated to be wholly disordered. The five eucaryotes were separated from bacteria and archaea by having the highest percentages of sequences predicted to have disordered segments > or = 50 in length: from 25% for Plasmodium to 41% for Drosophila. Estimates of wholly disordered proteins in the bacteria ranged from 1% to 8%, averaging to 3 +/- 2%, estimates in various archaea ranged from 2 to 11%, plus an apparently anomalous 18%, averaging to 7 +/- 5% that drops to 5 +/- 3% if the high value is discarded. Estimates in the 5 eucarya ranged from 3 to 17%. The putative wholly disordered proteins were often ribosomal proteins, but in addition about equal numbers were of known and unknown function. Overall, intrinsic disorder appears to be a common, with eucaryotes perhaps having a higher percentage of native disorder than archaea or bacteria.
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Proteínas/química , Proteínas/genética , Animales , Biología Computacional , Bases de Datos de Proteínas , Genoma , Pliegue de Proteína , ProteomaRESUMEN
More than 6,000 amino acid sequence attributes were ranked by their conditional probabilities for indicating ordered or disordered protein structure. The top 10 each from several different groups of attributes were merged with still other attributes and then subjected to selection by logistic regression. Evidently, the determination of order or disorder results from the interplay among several attributes, such as average Coordination Number, aromatic content and the numbers of non-polar amino acids, all of which favor the ordered state, and others like Net Charge, Flexibility Index, and the presence of certain polar amino acids, all of which favor disorder. The top 12 selected attributes were used as inputs for artificial neural network (ANN) predictors. Five predictors were developed, compared with each other, and with previous work. The best of these shows substantially improved generalization compared to our previously published predictor.
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Proteínas/química , Proteínas/genética , Biología Computacional , Modelos Logísticos , Redes Neurales de la Computación , Probabilidad , Pliegue de Proteína , Curva ROCRESUMEN
Transformation-associated recombination (TAR) cloning allows entire genes and large chromosomal regions to be specifically, accurately, and quickly isolated from total genomic DNA. We report the first example of radial TAR cloning from the mouse genome. Tg.AC mice carry a zeta-globin promoter/v-Ha-ras transgene. Fluorescence in situ hybridization localized the transgene integrant as a single site proximal to the centromere of chromosome 11. Radial TAR cloning in yeast was utilized to create orientation-specific yeast artificial chromosomes (YACs) to explore the possibility that cis-flanking regions were involved in transgene expression. YACs containing variable lengths of 5' or 3' flanking chromosome 11 DNA and the Tg.AC transgene were specifically chosen, converted to bacterial artificial chromosomes (BACs), and assayed for their ability to promote transcription of the transgene following transfection into an FVB/N carcinoma cell line. A transgene-specific reverse transcription-polymerase chain reaction assay was utilized to examine RNA transcripts from stably transfected clones. All Tg.AC BACs expressed the transgene in this in vitro system. This report describes the cloning of the v-Ha-ras transgene and suggests that transcriptional activity may not require cis elements flanking the transgene's integration site.