Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts

Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage genomes carry and express host-like photosynthesis genes, presumably to augment the host photosynthetic machinery during infection. To study the prevalence and evolutionary dynamics of this phenomenon, 33 cultured cyanophages of known family and host range and viral DNA from field samples were screened for the presence of two core photosystem reaction center genes, psbA and psbD. Combining this expanded dataset with published data for nine other cyanophages, we found that 88% of the phage genomes contain psbA, and 50% contain both psbA and psbD. The psbA gene was found in all myoviruses and Prochlorococcus podoviruses, but could not be amplified from Prochlorococcus siphoviruses or Synechococcus podoviruses. Nearly all of the phages that encoded both psbA and psbD had broad host ranges. We speculate that the presence or absence of psbA in a phage genome may be determined by the length of the latent period of infection. Whether it also carries psbD may reflect constraints on coupling of viral- and host-encoded PsbA–PsbD in the photosynthetic reaction center across divergent hosts. Phylogenetic clustering patterns of these genes from cultured phages suggest that whole genes have been transferred from host to phage in a discrete number of events over the course of evolution (four for psbA, and two for psbD), followed by horizontal and vertical transfer between cyanophages. Clustering patterns of psbA and psbD from Synechococcus cells were inconsistent with other molecular phylogenetic markers, suggesting genetic exchanges involving Synechococcus lineages. Signatures of intragenic recombination, detected within the cyanophage gene pool as well as between hosts and phages in both directions, support this hypothesis. The analysis of cyanophage psbA and psbD genes from field populations revealed significant sequence diversity, much of which is represented in our cultured isolates. Collectively, these findings show that photosynthesis genes are common in cyanophages and that significant genetic exchanges occur from host to phage, phage to host, and within the phage gene pool. This generates genetic diversity among the phage, which serves as a reservoir for their hosts, and in turn influences photosystem evolution.
The Iron- and Temperature-RegulatedcjrBC Genes of Shigella and Enteroinvasive Escherichia coli Strains Code for Colicin Js Uptake

ABSTRACT A cosmid library of DNA from colicin Js-sensitive enteroinvasiveEscherichia coli (EIEC) strain O164 was made in colicin Js-resistant strain E. coli VCS257, and colicin Js-sensitive clones were identified. Sensitivity to colicin Js was associated with the carriage of a three-gene operon upstream of and partially overlapping senB. The open reading frames were designated cjrABC (for colicin Js receptor), coding for proteins of 291, 258, and 753 amino acids, respectively. Tn7 insertions in any of them led to complete resistance to colicin Js. A near-consensus Fur box was found upstream ofcjrA, suggesting regulation of the cjroperon by iron levels. CjrA protein was homologous to iron-regulatedPseudomonas aeruginosa protein PhuW, whose function is unknown; CjrB was homologous to the TonB protein fromPseudomonas putida; and CjrC was homologous to a putative outer membrane siderophore receptor from Campylobacter jejuni. Cloning experiments showed that the cjrBand cjrC genes are sufficient for colicin Js sensitivity. Uptake of colicin Js into sensitive bacteria was dependent on the ExbB protein but not on the E. coli K-12 TonB and TolA, -B, and -Q proteins. Sensitivity to colicin Js is positively regulated by temperature via the VirB protein and negatively controlled by the iron source through the Fur protein. Among EIEC strains, two types of colicin Js-sensitive phenotypes were identified that differed in sensitivity to colicin Js by 1 order of magnitude. The difference in sensitivity to colicin Js is not due to differences between the sequences of the CjrB and CjrC proteins.
Disulfide bond-mediated multimerization of Ask 1 and its reduction by thioredoxin-1 regulate H 2 O 2-induced JNK activation and apoptosis

Apoptosis signal regulated kinase-1 (Ask1) lies upstream of a major redox-sensitive pathway leading to the activation of Jun N-terminal kinase (JNK) and the induction of apoptosis. We found that cell exposure to H2O2 caused the rapid oxidation of Ask1 leading to its multimerization through the formation of interchain disulfide bonds. Oxidized Ask1 was fully reduced within minutes after induction by H2O2. During this reduction, the thiol-disulphide oxidoreductase thioredoxin-1 (Trx1) became covalently associated with Ask1. Overexpression of Trx1 accelerated the reduction of Ask1 and a redox-inactive mutant of Trx1 (C35S) remained trapped with Ask1 blocking its reduction. Preventing the oxidation of Ask1 by either overexpressing Trx1 or using an Ask1 mutant in which the sensitive cysteines were mutated (Ask1Cys), impaired the activation of JNK and the induction of apoptosis while having little effect on Ask1 activation. Those results indicate that Ask1 oxidation is required at a step subsequent to activation for signalling downstream of Ask1 after H2O2-treatment.
Complementary strand relocation may play vital roles in RecA-based homology recognition

RecA-family proteins mediate homologous recombination and recombinational DNA repair through homology search and strand exchange. Initially, the protein forms a filament with the incoming single-stranded DNA (ssDNA) bound in site I. The RecA–ssDNA filament then binds double-stranded DNA (dsDNA) in site II. Non-homologous dsDNA rapidly unbinds, whereas homologous dsDNA undergoes strand exchange yielding heteroduplex dsDNA in site I and the leftover outgoing strand in site II. We show that applying force to the ends of the complementary strand significantly retards strand exchange, whereas applying the same force to the outgoing strand does not. We also show that crystallographically determined binding site locations require an intermediate structure in addition to the initial and final structures. Furthermore, we demonstrate that the characteristic dsDNA extension rates due to strand exchange and free RecA binding are the same, suggesting that relocation of the complementary strand from its position in the intermediate structure to its position in the final structure limits both rates. Finally, we propose that homology recognition is governed by transitions to and from the intermediate structure, where the transitions depend on differential extension in the dsDNA. This differential extension drives strand exchange forward for homologs and increases the free energy penalty for strand exchange of non-homologs.
The genetics of exercise behavior and psychological well-being

Waarom vinden sommige mensen het heerlijk om uren door het bos hard te lopen, terwijl andere mensen liever computeren of tv kijken? Door vragenlijsten af te nemen bij eeneiige en twee-eiige tweelingen concludeert Janine Stubbe in haar proefschrift dat in de adolescentie verschillen in sportgedrag hoofdzakelijk verklaard worden door omgevingsinvloeden. Vanaf 18 jaar gaan genen een grote rol spelen in variatie in sportgedrag. Welke genen veroorzaken de verschillen in de behoefte aan sporten? Mogelijk beleeft niet iedereen even veel plezier aan sport wat veroorzaakt kan worden door genen. In een vervolgonderzoek is onderzocht of er een verband bestaat tussen sportgedrag en het psychologische welbevinden. Hieruit blijkt dat sporters meer tevreden zijn met hun leven en zich gelukkiger voelen dan mensen die niet sporten. Dit is het eerste grootschalige onderzoek dat bevestigd dat sporten gerelateerd is aan een hoger positief welbevinden en niet alleen aan minder depressie. Vervolgens is onderzocht hoe deze relatie tussen sportgedrag en welbevinden tot stand is gekomen. Het blijkt dat beide eigenschappen worden be? oed door dezelfde genen. Dit betekent dat de genen die variatie in sportgedrag verklaren ook gedeeltelijk individuele verschillen in positief welbevinden verklaren. Mogelijk is het niet voor iedereen in aanleg weggelegd om sporten als prettig te ervaren. Om mensen aan het bewegen te krijgen lijkt het belangrijk om een individuele aanpak te hanteren. Op deze manier kan gekeken worden welke sportieve activiteit het beste bij een persoon past, zodat meer mensen met plezier sportief bezig zijn.
GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins

After extra-cellular stimulation of G-Protein Coupled Receptors (GPCRs), GDP/GTP exchange appears as the key, rate limiting step of the intracellular activation cycle of heterotrimeric G-proteins. Despite the availability of a large number of X-ray structures, the mechanism of GDP release out of heterotrimeric G-proteins still remains unknown at the molecular level. Starting from the available X-ray structure, extensive unconstrained/constrained molecular dynamics simulations were performed on the complete membrane-anchored Gi heterotrimer complexed to GDP, for a total simulation time overcoming 500 ns. By combining Targeted Molecular Dynamics (TMD) and free energy profiles reconstruction by umbrella sampling, our data suggest that the release of GDP was much more favored on its phosphate side. Interestingly, upon the forced extraction of GDP on this side, the whole protein encountered large, collective motions in perfect agreement with those we described previously including a domain to domain motion between the two ras-like and helical sub-domains of Gα.
Radiation and SN38 treatments modulate the expression of microRNAs, cytokines and chemokines in colon cancer cells in a p53-directed manner

Aberrant expression of miRNAs, cytokines and chemokines are involved in pathogenesis of colon cancer. However, the expression of p53 mediated miRNAs, cyto- and chemokines after radiation and SN38 treatment in colon cancer remains elusive. Here, human colon cancer cells, HCT116 with wild-type, heterozygous and a functionally null p53, were treated by radiation and SN38. The expression of 384 miRNAs was determined by using the TaqMan® miRNA array, and the expression of cyto- and chemokines was analyzed by Meso-Scale-Discovery instrument. Up- or down-regulations of miRNAs after radiation and SN38 treatments were largely dependent on p53 status of the cells. Cytokines, IL-6, TNF-α, IL-1β, Il-4, IL-10, VEGF, and chemokines, IL-8, MIP-1α were increased, and IFN-γ expression was decreased after radiation, whereas, IL-6, IFN-γ, TNF-α, IL-1β, Il-4, IL-10, IL-8 were decreased, and VEGF and MIP-1α were increased after SN38 treatment. Bioinformatic analysis pointed out that the highly up-regulated miRNAs, let-7f-5p, miR-455-3p, miR-98, miR-155-5p and the down-regulated miRNAs, miR-1, miR-127-5p, miR-142-5p, miR-202-5p were associated with colon cancer pathways and correlated with cyto- or chemokine expression. These miRNAs have the potential for use in colon cancer therapy as they are related to p53, pro- or anti-inflammatory cyto- or chemokines after the radiation and SN38 treatment.
ACE inhibitors after myocardial infarction.

EDITOR,-Correspondence concerning liver failure induced by paracetamol has suggested that education regarding the potential dangerousness of the drug in overdose may prevent deaths. "2 Though increased public awareness of this issue may well reduce the number of accidental deaths, recent experience confirms Gary P Bray's fear that it could paradoxically encourage more people to take an overdose. ' In addition to being excellent drama, BBC television's long running series Casualty sees itself as having a health education role. To this end, the episode on 9 January sought to highlight the problem of deliberate self harm by paracetamol overdosage. In the programme a 15 year old girl presented to the accident and emergency department some 48 hours after ingesting about 50 tablets of paracetamol. Her motives were sympathetically presented: she was certainly not suicidal, merely a fairly typical teenage girl with domestic and school stresses. By the time of presentation she had abdominal pain and vomiting. Results of liver function tests were described as being grossly raised, and the programme ended with her having entered a coma and being transferred to the regional liver unit, the casualty consultant clearly stating that she was probably going to die. The subject was handled sensitively and was obviously intended to serve as a deterrent to any adolescent viewers contemplating taking "just a few tablets" to highlight one of the many grievances faced in the average teenager's life.
The incidence of dieting amongst adolescent girls: a question of interpretation?

AIM It is the intention of this study establish the extent of dieting practices amongst adolescent girls and identify their perceptions with regard to 'dieting' and 'healthy eating'. METHODS A total of 140 girls, aged 12-13 years, were recruited from two schools. A self-reported questionnaire, which determined the incidence of dieting and sought to identify the girls' perceptions of 'dieting' and 'healthy eating', was used to collect data. RESULTS Out of the total group, 33.6% reported that they had dieted at some time and 15.8% were presently dieting. The most popular definition of dieting amongst the dieters was 'eating less/cutting down'; however, the second most popular answer was 'eating healthy food' which was the most popular answer amongst the non-dieters. The most popular definition of healthy eating was 'increasing fruit/ veg/salads', which is similar to how many girls perceived dieting, i.e. eating healthy food (fruit/veg/salads). CONCLUSION Establishing the actual incidence of dieting amongst adolescent girls is not a clear-cut issue as it can be interpreted in many different ways, depending on the perceptions of the individual. The results of this study showed that in many cases 'dieting' and 'healthy eating' were perceived in a similar light, concluding that the dietary intake of dieters may be similar to that of non-dieters with both groups being at risk from any related health problems.
How to lower postoperative complications after radical cystectomy – a review

Introduction Lowering morbidity and mortality after RC is subject of considerable interest. Lately, many evidence-based data on improvements in operative technique, anesthetic management, and patient care have been published. In this article, we present a review of literature on how to lower postoperative complications after RC. Material and methods The Medline, and Web of Science databases were searched without a time limit on February 2016 using the terms ‘cystectomy’ in conjunction with ‘radical’, ‘bladder cancer’, ‘complications’ or ‘management’. Boolean operators (NOT, AND, OR) were also used in succession to narrow and broaden the search. The search was limited to the English, Polish and Spanish literature. Results Many complications may be avoided by appropriate patient selection and meticulous introduction of care protocols. Conclusions RC as treatment free of complications, even in the hands of an experienced urologist, does not exist. A large number of complications are acceptable in the name of good long-term results. Optimum results are possible with proper surgical technique, good patients and urinary diversion selection and proper patient management in the pre-, peri, and postoperative period.
Nucleolar structure and function are regulated by the deubiquitylating enzyme USP36

The nucleolus is a subnuclear compartment and the site of ribosome biogenesis. Previous studies have implicated protein ubiquitylation in nucleolar activity. Here we show that USP36, a deubiquitylating enzyme of unknown function, regulates nucleolar activity in mammalian cells. USP36 localized to nucleoli via the C-terminal region, which contains basic amino acid stretches. Dominant-negative inhibition of USP36 caused the accumulation of ubiquitin-protein conjugates in nucleoli, suggesting that nucleoli are the site of USP36 action. USP36 deubiquitylated the nucleolar proteins nucleophosmin/B23 and fibrillarin, and stabilized them by counteracting ubiquitylation-mediated proteasomal degradation. RNAi-mediated depletion of cellular USP36 resulted in reduced levels of rRNA transcription and processing, a less-developed nucleolar morphology and a slight reduction in the cytoplasmic ribosome level, which eventually led to a reduced rate of cell proliferation. We conclude that by deubiquitylating various nucleolar substrate proteins including nucleophosmin/B23 and fibrillarin, USP36 plays a crucial role in regulating the structure and function of nucleoli.
PEARL OYSTERS

An account of the pearl oyster resources with a brief note on biology, collection methods, seed production and conservation and management in the Indian subcontinent is dealt with in this paper. Both in the Gulf of Kutch and the Gulf of Mannar, the population does not show improvement. Conservation and management of this important resource in the light of the present R&D carried out by the CMFRI is discussed. Enhancement of the wild stock through the production of genetically improved seed in the hatchery and ranching them to selected beds and close monitoring of the physico-chemical and biological factors over a period of time is suggested. Farming of oysters on the natural beds can enhance the pearl quality and may form a breeding reserve.
PLANN-CR-ARD model predictions and Non-parametric estimates with Confidence Intervals

This paper investigates the performance of the PLANN-CR-ARD network predictions through a comparison with the confidence intervals and the non-parametric estimates obtained from the survival analysis of a Primary Billiary Cirrhosis (PBC) dataset. The predictions of the PLANN-CR-ARD model are marginalized using two methods: approximation of the integral of marginalization and the Monte Carlo method. The numerical results show that the PLANN-CR-ARD predicts very well, the results being situated within the confidence intervals of the non-parametric estimates. The Model Selection is also performed on the same dataset. The PLANN-CR-ARD can be used to explore the non-linear interdependencies between the predicted outputs and the input data which in survival analysis describes the characteristics of the patients.
ASSORTATIVE MATING IN POISON-DART FROGS BASED ON AN ECOLOGICALLY IMPORTANT TRAIT

Abstract The origin of new species can be influenced by both deterministic and stochastic factors. Mate choice and natural selection may be important deterministic causes of speciation (as opposed to the essentially stochastic factors of geographic isolation and genetic drift). Theoretical models predict that speciation is more likely when mate choice depends on an ecologically important trait that is subject to divergent natural selection, although many authors have considered such mating/ecology pleiotropy, or “magic-traits” to be unlikely. However, phenotypic signals are important in both mate choice and ecological processes such as avoiding predation. In chemically defended species, it may be that the phenotypic characteristics influencing mate choice are the same signals being used to transmit a warning to potential predators, although few studies have demonstrated this in wild populations. We tested for assortative mating between two color morphs of the Strawberry Poison-Dart Frog, Dendrobates pumilio, a group with striking geographic variation in aposematic color patterns. We found that females significantly prefer individuals of their own morph under two different light treatments, indicating strong assortative mating based on multiple coloration cues that are also important ecological signals. This study provides a rare example of one phenotypic trait affecting both ecological viability and nonrandom mating, indicating that mating/ecology pleiotropy is plausible in wild populations, particularly for organisms that are aposematically colored and visually orienting.
Neuroscience and Biobehavioral Reviews

Oral somatosensory awareness refers to the somatic sensations arising within the mouth, and to the information these sensations provide about the state and structure of the mouth itself, and objects in the mouth. Because the oral tissues have a strong somatosensory innervation, they are the locus of some of our most intense and vivid bodily experiences. The salient pain of toothache, or the habit of running one’s tongue over one’s teeth when someone mentions “dentist”, provide two very different indications of the power of oral somatosensory awareness in human experience and behaviour. This paper aims to review the origins and structure of oral somatosensory awareness, focussing on quantitative, mechanistic studies in humans. We ﬁrst extend a model of levels of bodily awareness to the speciﬁc case of the mouth. We then brieﬂy summarise the sensory innervation of oral tissues, and their projections in the brain. We next describe how these peripheral inputs give rise to perceptions of objects in the mouth, such as foods, liquids and oral devices, and also of the mouth tissues themselves. Finally, we consider the concept of a conscious mouth image, and the somatosensory basis of “mouth feel”. The theoretical framework outlined in this paper is intended to facilitate scientiﬁc studies of this important site of human experience. © 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
Hypomelanosis of Ito: Report of two cases

Hypomelanosis of Ito is a neurocutaneous disorder characterized by hypopigmented whorls, streaks and patches distributed along the lines of Blaschko, often associated with neurological and musculoskeletal abnormalities. We herein report two patients belonging to ethnic Kashmiri origin with this disorder.
Treatment of human brucellosis with doxycycline and gentamicin

The objective of the present prospective, noncomparative, multicenter study was assess the safety and efficacy of gentamicin and doxycycline therapy for human brucellosis. In the first part of the study, a cohort of 17 patients received 100 mg of doxycycline (or 50 mg/kg of body weight per day if the body weight was < 40 kg) orally every 12 h for 45 days (cohort 1). In the second part of the study a subsequent cohort of 35 patients was treated with doxycycline at the same dosage for 30 days (cohort 2). All patients were treated intramuscularly with gentamicin at 240 mg (or 5 mg/kg per day if the body weight was < 50 kg) once daily for the first 7 days. Both cohorts showed a favorable response during therapy, and there were no therapeutic failures. Relapse was noted in 1 (5.9%; 95% confidence interval [95% CI], 0.15 to 28.7%) of the 17 patients in cohort 1 and in 8 (22.9%; 95% CI, 10.4 to 40.1%) of the 35 patients in cohort 2. Nineteen patients (36.5%; 95% CI, 23.6 to 51.0%) had adverse effects, with no differences between cohorts, and no patients had a treatment-limiting adverse effect. The study indicates that the combination of doxycycline for 45 days and gentamicin for 7 days is an effective and well-tolerated therapy for human brucellosis. The relapse rates obtained with doxycycline treatment for 30 days appear to be higher than those obtained with doxycycline treatment for 45 days.
A lover or a fighter? Opposing sexual selection pressures on men’s vocal pitch and facial hair

Lay Summary Men’s optimum masculinity depends on whether they want to attract partners or compete with rivals. We found that men’s voice pitch was most attractive around 1.5 standard deviations lower than average, whereas facial hair growth did not consistently affect attractiveness. In contrast, men were perceived ever more dominant with lower voices and more facial hair. Sexual selection consists of both attracting mates and competing against rivals, but here selection pressures might oppose each other somewhat.