The Russian invasion of Ukraine: a humanitarian tragedy and a tragedy for science

The Invasion of Ukraine prompts us to support our Ukranian colleagues but also to keep open communication with the Russian scientists who oppose the war.

In the eyes of the civilized world, Russia has already lost the war: politically, it is becoming ever more isolated; economically as the sanctions take an enormous toll; militarily as the losses of the Russian army mount. In contrast, the courage of Ukrainian people fighting for their independence has united the Western world that is providing enormous support for those Ukrainians who fight the Russian invasion and those who have fled their war‐torn country. Once this war is over, Ukraine will have to heal the wounds of war, reunite families, restore its economy, reestablish infrastructure, and rebuild science and education. Russia will have to restore its dignity and overcome its self‐inflicted isolation.Europe’s unity in condemning Russia’s war of aggression and showing its solidarity with Ukraine has been impressive. This includes not the least welcoming and accommodating millions of refugees. We, the scientific community in Europe, have a moral obligation to help Ukrainian students and colleagues by providing safe space to study and to continue their research. First, European research organizations and funding agencies should develop strategies to support them in the years to come. Second, efforts by EMBO, research funders, universities, and research institutions to support Ukrainian students and scientists are necessary. As a first priority, dedicated and unbureaucratic short‐term scholarship and grant programs are required to accommodate Ukrainian scientists; such programs have been already initiated by many organizations, for example, by EMBO, Volkswagen Stiftung, Max Planck Society, and the ERC among others. These help Ukrainian scientists to stay connected to research and become integrated into the European research landscape. In the long‐term and after the war, this aid should be complemented by funding for research centers of excellence in Ukraine, to which scientists could then return.Even though the priority must be to help Ukrainians, we must also think of students and colleagues in Russia who oppose the war and are affected by the sanctions. As the Iron Curtain closes again, we have to think differently about our ongoing and future collaborations. Although freezing most, if not all, research collaborations with official Russian organizations is justified, it would be a mistake to extend these sanctions to all scientists and students. There is already an exodus of Russian and Belarusian scholars, which will only accelerate in the next months and years, and accepting scientists who ask for political asylum will be beneficial for Europe.The fraction of Russian society in open opposition to the war is, unfortunately, smaller than that officially in support of it. At the beginning of the war, a number of Russian scientists published an open letter on the internet, in which they condemn this war (https://t‐invariant.org/2022/02/we‐are‐against‐war/). They clearly state that "The responsibility for unleashing a new war in Europe lies entirely with Russia. There is no rational justification for this war”, and “demand an immediate halt to all military operations directed against Ukraine". At the same time, other prominent Russian science and education officials signed the “Statement of the Russian Union of University Rectors (Provosts)”, which expressed unwavering support for Russia, its president and its Army and their goal to “to achieve demilitarization and denazification of Ukraine and thus to defend ourselves from the ever‐growing military threat” (https://www.rsr‐online.ru/news/2022‐god/obrashchenie‐rossiyskogo‐soyuza‐rektorov1/).Inevitably, Russian scientists must decide themselves how to live and continue their scientific work under the increasingly tight surveillance of the Kremlin regime. History is repeating itself. Not long ago, during the Cold War, Soviet scientists were largely isolated from the international research community and worked in government‐controlled research. In some fields, no one knew what they were working on or where. However, even in those dark times, courageous individuals such as Andrei Sakharov spoke out against the regime and tried to educate the next generation about the importance of free will. Many Soviet geneticists had been arrested under Stalin’s regime of terror and as a result of Lysenkoism and were executed or sent to the Gulag or had to emigrate, such as Nikolaj Timofeev‐Resovskij, one of the great geneticists of his time and an opponent of communism. As a result of sending dissident scientists to Siberia, great educational institutions were created in the region, which trained many famous scientists. History tells us that it is impossible to kill free will and the search for truth.The Russian invasion of Ukraine is a major humanitarian tragedy and a tragedy for science at many levels. Our hope is that the European science community, policymakers, and funders will be prepared to continue and expand support for our colleagues from Ukraine and eventually help to rebuild the bridges with Russian science that have been torn down.This commentary has been endorsed and signed by the EMBO Young Investigators and former Young Investigators listed below.

All signatories are current and former EMBO Young Investigators and endorse the statements in this article.

Does an Eye-Hand Coordination Test Have Added Value as Part of Talent Identification in Table Tennis? A Validity and Reproducibility Study

This study investigated the added value, i.e. discriminative and concurrent validity and reproducibility, of an eye-hand coordination test relevant to table tennis as part of talent identification. Forty-three table tennis players (7–12 years) from national (n = 13), regional (n = 11) and local training centres (n = 19) participated. During the eye-hand coordination test, children needed to throw a ball against a vertical positioned table tennis table with one hand and to catch the ball correctly with the other hand as frequently as possible in 30 seconds. Four different test versions were assessed varying the distance to the

Perioperative Opioid Counseling Reduces Opioid Use Following Primary Total Joint Arthroplasty

BackgroundPreoperative counseling may reduce postoperative opioid requirements; however, there is a paucity of randomized controlled trials (RCTs) demonstrating efficacy. The purpose of this study was to perform an interventional, telehealth-based RCT evaluating the effect of peri-operative counseling on quantity and duration of opioid consumption following primary total joint arthroplasty (TJA).MethodsParticipants were randomized into three groups: 1. Control group, no perioperative counseling; 2. Intervention group, preoperative educational video; 3. Intervention group, preoperative educational video and postoperative acceptance and commitment therapy (ACT). Opioid consumption was evaluated daily for 14 days and at 6 weeks postoperatively. Best-case and worse-case intention to treat analyses were performed to account for non-responses. Bonferroni corrections were applied.Results183 participants were analyzed (63 in Group 1, 55 in Group 2, and 65 in Group 3). At 2 weeks postoperatively, there was no difference in opioid consumption between Groups 1, 2, and 3 (p>0.05 for all). At 6 weeks postoperatively, Groups 2 and 3 had consumed significantly less opioids than Group 1 (p=0.04, p<0.001) (VariableGroupp-value1. Control2. Video OnlyVideo + ACTSex (n, % female)39 (62%)32 (58%)40 (62%)0.90Surgery (n, % THA)26 (41%)21 (38%)31 (47%)0.56Age (mean ± SD; years)59 ± 1159 ± 1158 ± 9Overall: 0.83
1v2: 0.98
2v3: 0.65
2v3: 0.56Prolonged Opioid Use > 60 mo. (n, %)000-Opioid Use Within 3 mo. of Index Surgery (n, %)0 (14%)4 (7%)5 (8%)0.34Open in a separate windowSD – standard deviation.Table 2.Quantity of Opioid Consumption at 2 Weeks Postoperatively, Best-Case Scenario

Vast (but avoidable) underestimation of global biodiversity

The number of species on Earth is highly uncertain. A recent study has suggested that there are less than 2 million prokaryotic species on Earth; this Formal Comment suggests instead that there are more likely hundreds of millions or billions of species, and that the majority of these are bacteria associated with insects and other animals.

The number of species on Earth is a fundamental number in science. Yet, estimates of global biodiversity have been highly uncertain. There are presently approximately 1.9 million described species [1]. Estimates of the actual number (both described and undescribed) have ranged from the low millions into the trillions [2,3]. Furthermore, described species richness [1] is dominated by animals (1.3 million; 68%), not bacteria (approximately 10,000 species; 0.5%). Larsen and colleagues [2] summarized evidence suggesting that the majority of species on Earth may be bacteria associated with insect hosts and that bacterial richness may push global biodiversity into the hundreds of millions of species or even low billions.Louca and colleagues [4] (LEA hereafter) have claimed instead that there are only 40,100 host-associated bacterial species among all animal species and 0.8 to 1.6 million prokaryotic species overall (see their “Author summary”). Strangely, they excluded bacterial species associated with animal hosts from their estimates of total prokaryotic diversity and justified this by claiming that the estimates of Larsen and colleagues [2] were “mathematically flawed.” Here, I examine their claims and present new estimates of global biodiversity.Remarkably, all projections by LEA for host-associated bacterial richness were based on an estimate from one ant genus (Cephalotes), an estimate that is demonstrably incorrect by orders of magnitude (S1 Text). Without examining the underlying data [5], LEA estimated only 40 bacterial species among all 130 ant species in this genus. Yet, simply counting the bacterial species among the 25 sampled ant species in that genus reveals 616 unique bacterial species, of which 539 appear to be unique to the genus and 369 each unique to a single ant species (using the standard 97% cutoff for 16S divergence and data from [5]). Thus, there were >500 bacterial species among 25 ant species, not 40 bacterial species among 130 ant species. This mistake was further exacerbated by inexplicably ignoring data from the other 2 insect genera analyzed by Larsen and colleagues [2], thus maximizing the impact of their incorrect estimate for this genus.Their overall estimate of bacterial richness was also strongly influenced by their questionable assumption that all animal genera can share bacterial species (i.e., reducing their estimate of 3 million host-associated bacterial species to only 40,100). They assumed “a conservative overlap of only 0.1% between any two randomly chosen genera” for the number of bacterial species shared between animal genera. No justification was given for this value of 0.1%, nor were any alternative values explored. Furthermore, they implicitly assumed that any bacterial species can be shared between any pair of animal genera, regardless of their phylogeny, habitat, or geographic range. So, for example, a bacterial species that is a gut endosymbiont of a terrestrial herbivorous insect species endemic to Madagascar could somehow be shared with a deep-sea worm in the northern Pacific Ocean. This is ridiculous: there must be a reason why bacterial species are shared among host species and genera (e.g., shared phylogeny, location, diet). For example, broad-scale studies show that sharing of bacteria among insect hosts is associated with both host phylogeny and diet [6].LEA stated “it is known that substantial overlap exists between the microbiota of different host genera and even of distantly related animal taxa.” However, they provided no numbers to justify this “substantial overlap.” In fact, none of the papers they cited as supporting this assumption actually do (S2 Text). For example, one study [7] found 5 bacterial species shared among 5 insect genera utilizing the same type of host plant (cycads). However, LEA do not mention that this study found 1,789 unique bacterial species among just these 5 insect species (or 177 after filtering). This seems inconsistent with their estimate of only 40,100 bacterial species across all animals. In summary, rather than estimating the overlap of bacterial species among host genera, LEA simply made a number up and combined this with unrealistic, unsupported assumptions about overlap. If LEA had considered Cephalotes (which all their estimates were based on), a survey of this genus and related genera [5] found 1,019 bacterial species, with only 77 of the 616 bacterial species in Cephalotes shared with other sampled genera, and the sharing of bacterial species among hosts strongly related to host phylogeny.Numerous surveys of bacterial diversity in insects strongly suggest that there are far more than 40,100 bacterial species among all animals (8] found roughly twice as many bacterial species as those of approximately 30 insect species [5,9], and the study of 218 insect species [6] found >3.5 times as many as the study of 62 insect species. The simple fact that a study found 9,301 bacterial species among only 218 sampled insect species strongly suggests that there are more than 40,100 bacteria among all animals.Table 1Surveys of bacterial diversity among insect species.LEA incorrectly estimated that a genus of 130 ant species (Cephalotes) hosts only 40 bacterial species and subsequently assumed that all animal genera have the same low number of bacterial species. These broad surveys of bacterial species among insects suggest that many insects (including Cephalotes) host much larger numbers of bacterial species.

Cognitive Manic Symptoms in Bipolar Disorder Associated with Polymorphisms in the DAOA and COMT Genes

Introduction

Bipolar disorder is characterized by severe mood symptoms including major depressive and manic episodes. During manic episodes, many patients show cognitive dysfunction. Dopamine and glutamate are important for cognitive processing, thus the COMT and DAOA genes that modulate the expression of these neurotransmitters are of interest for studies of cognitive function.

Methodology

Focusing on the most severe episode of mania, a factor was found with the combined symptoms of talkativeness, distractibility, and thought disorder, considered a cognitive manic symptoms (CMS) factor. 488 patients were genotyped, out of which 373 (76%) had talkativeness, 269 (55%) distractibility, and 372 (76%) thought disorder. 215 (44%) patients were positive for all three symptoms, thus showing CMS (Bipolar disorder type 1 [n]488Men [n (%)]209 (43)Talkativeness [n (%)]373 (76)Distracibility [n (%)]269 (55)Thought disorder [n (%)]372 (76)Cognitive manic symptoms^* [n (%)]215 (44)Men [n (%)]81 (39)Non-Cognitive manic symptoms [n (%)]248 (51)Men [n (%)]117 (56)Unknown [n (%)]25 (5)Men [n (%)]11 (44)Anonymous blood donors (ABD)1044Men [n (%)]616 (59)Open in a separate window^*having all three symptoms: talkativeness, distractibility, and tought disorder.

Results

The finding of this study was that cognitive manic symptoms in patients with bipolar 1 disorder was associated with genetic variants in the DAOA and COMT genes. Nominal association for DAOA SNPs and COMT SNPs to cognitive symptoms factor in bipolar 1 disorder was found in both allelic (BP1 CMSBP1 non-CMSABDBP1 CMS vs. non-CMS^b BP1 CMS vs. ABD controls^b GeneSNP^a aa/ab/bbaa/ab/bbaa/ab/bbpEMP1^c EMP2^d OR [95% CI] ^e pEMP1^c EMP2^d OR [95% CI] ^e DAOA rs3916967 (C/T)32/88/8950/118/77177/494/3610.0180.0180.210.72 [0.55–0.93]0.0290.0260.280.78 [0.66–1.0] DAOA rs2391191 (A/C)28/75/7939/111/70179/487/3570.0550.0390.500.75 [0.57–1.0]0.0200.0190.210.75 [0.63–1.0] DAOA rs1935062 (C/A)26/67/8935/102/86146/460/4050.120.120.780.80 [0.58–1.0]0.0690.0660.520.80 [0.65–1.0] COMT rs5993883 (T/G)33/120/5371/112/57269/510/2230.0250.0300.270.73 [0.56–0.95]0.0017^* 1.0E^{−4 *} 0.021^* 0.68 [0.91–1.4] COMT rs165599 (G/A)29/94/8725/93/12687/443/5010.0930.0940.691.27 [1.0–1.8]0.0140.0170.161.34 [1.1–1.7]Open in a separate window^aSNP (minor allele(a)/major allele(b)).^bgender and rs1718119 as covariate.^cpoint-wise p-value from 10,000 pemutations with no covarite (EMP1).^dcorrected empirical p-value by max (T) permutation.^eodds ratio (OR), the proportion of minor versus major allele affected (cognitive manic symptoms factor)/proportion of minor versus major allele unaffected (non-cognitive manic symptoms factor or ABD controls).^*significant after correction for multiple testing by max (T) permutation.

Table 3

Haplotype association of haplotype group 1 in bipolar 1 patients with cognitive manic symptoms (CMS) compared with non-CMS patients or ABD controls in the DAOA gene.

Economic Benefits of Investing in Women’s Health: A Systematic Review

Background

Globally, the status of women’s health falls short of its potential. In addition to the deleterious ethical and human rights implications of this deficit, the negative economic impact may also be consequential, but these mechanisms are poorly understood. Building on the literature that highlights health as a driver of economic growth and poverty alleviation, we aim to systematically investigate the broader economic benefits of investing in women’s health.

Methods

Using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, we systematically reviewed health, gender, and economic literature to identify studies that investigate the impact of women’s health on micro- and macroeconomic outcomes. We developed an extensive search algorithm and conducted searches using 10 unique databases spanning the timeframe 01/01/1970 to 01/04/2013. Articles were included if they reported on economic impacts stemming from changes in women’s health (table of outcome measures included in full review, Outcome measures   FertilityIntergenerational Health SpilloverEducationProductivitySavingsMicroeconomic level    Total fertility rateChild survivalEnrollment in schoolIncomeMoneyChange in fertilityChild wellbeing and behaviorYears of schoolingPurchasing powerAssetsAge at first birth/ teenage pregnanciesAnthropometryEarly drop outPerformanceBirth spacingImproved cognitive developmentPerformance in school Life expectancyHigher education  Adult health outcomesLiteracy  Nutrition   Intrauterine growth  Macroeconomic level    Open in a separate windowGross domestic product/gross national product, gross domestic product/gross national product growth, income per capita, labor force participation, per capita income.

Results

The existing literature indicates that healthier women and their children contribute to more productive and better-educated societies. This study documents an extensive literature confirming that women’s health is tied to long-term productivity: the development and economic performance of nations depends, in part, upon how each country protects and promotes the health of women. Providing opportunities for deliberate family planning; healthy mothers before, during, and after childbirth, and the health and productivity of subsequent generations can catalyze a cycle of positive societal development.

Conclusions

This review highlights the untapped potential of initiatives that aim to address women’s health. Societies that prioritize women’s health will likely have better population health overall, and will remain more productive for generations to come.     

Immunological Mechanisms Mediating Hantavirus Persistence in Rodent Reservoirs

Hantaviruses, similar to several emerging zoonotic viruses, persistently infect their natural reservoir hosts, without causing overt signs of disease. Spillover to incidental human hosts results in morbidity and mortality mediated by excessive proinflammatory and cellular immune responses. The mechanisms mediating the persistence of hantaviruses and the absence of clinical symptoms in rodent reservoirs are only starting to be uncovered. Recent studies indicate that during hantavirus infection, proinflammatory and antiviral responses are reduced and regulatory responses are elevated at sites of increased virus replication in rodents. The recent discovery of structural and non-structural proteins that suppress type I interferon responses in humans suggests that immune responses in rodent hosts could be mediated directly by the virus. Alternatively, several host factors, including sex steroids, glucocorticoids, and genetic factors, are reported to alter host susceptibility and may contribute to persistence of hantaviruses in rodents. Humans and reservoir hosts differ in infection outcomes and in immune responses to hantavirus infection; thus, understanding the mechanisms mediating viral persistence and the absence of disease in rodents may provide insight into the prevention and treatment of disease in humans. Consideration of the coevolutionary mechanisms mediating hantaviral persistence and rodent host survival is providing insight into the mechanisms by which zoonotic viruses have remained in the environment for millions of years and continue to be transmitted to humans.Hantaviruses are negative sense, enveloped RNA viruses (family: Bunyaviridae) that are comprised of three RNA segments, designated small (S), medium (M), and large (L), which encode the viral nucleocapsid (N), envelope glycoproteins (G_N and G_C), and an RNA polymerase (Pol), respectively. More than 50 hantaviruses have been found worldwide [1]. Each hantavirus appears to have coevolved with a specific rodent or insectivore host as similar phylogenetic trees are produced from virus and host mitochondrial gene sequences [2]. Spillover to humans causes hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS), depending on the virus [3]–[5]. Although symptoms vary, a common feature of both HFRS and HCPS is increased permeability of the vasculature and mononuclear infiltration [4]. Pathogenesis of HRFS and HCPS in humans is hypothesized to be mediated by excessive proinflammatory and CD8+ T cell responses (​).

Table 1

Summary of Immune Responses in Humans during Hantavirus Infection.

Conventional transmission electron microscopy

Researchers have used transmission electron microscopy (TEM) to make contributions to cell biology for well over 50 years, and TEM continues to be an important technology in our field. We briefly present for the neophyte the components of a TEM-based study, beginning with sample preparation through imaging of the samples. We point out the limitations of TEM and issues to be considered during experimental design. Advanced electron microscopy techniques are listed as well. Finally, we point potential new users of TEM to resources to help launch their project.Transmission electron microscopy (TEM) has been an important technology in cell biology ever since it was first used in the early 1940s. The most frequently used TEM application in cell biology entails imaging stained thin sections of plastic-embedded cells by passage of an electron beam through the sample such that the beam will be absorbed and scattered, producing contrast and an image (see TermDefinitionBeem capsulePlastic forms that hold samples in resin during polymerizationBlocks (bullets)Polymerized samples in plastic removed from the Beem capsule and ready to sectionBlock faceSmall surface trimmed on a block before sectioningBoatWater reservoir in which sections float after being cut by a knifeCLEMCorrelative light and electron microscopyDehydrationRemoval of water from a sample by replacement with solventElectron tomography (ET)A method to image thick sections (200–300 nm) and produce three-dimensional imagesEmbeddingProcess of infiltrating the sample with resinFixationSample preservation with low temperature and/or chemicals to maintain sample integrityGridSmall metal support that holds the sections for viewing in the electron microscopeHPF/FSHigh-pressure freezing/freeze substitution sample preparation techniqueImmuno-EMDetection of proteins in EM samples using antibodiesIn-FXXKing credible!!!!Actual user quote in response to particularly beautiful sample. You may embellish with your own words.KnifeA very sharp edge, either glass or diamond, used to slice off resin-embedded samples into sectionsPre-embedding labelingApplication of antibodies before fixation and embeddingPost-embedding labelingApplication of antibodies to sections on the gridPoststainingStaining with heavy metals of sections on a gridResinLiquid form of the plastics used for embeddingRibbonCollection of serial sections placed on the gridSerials sectionsOne-after-the-other thin sections in a ribbonTEMTransmission electron microscopyThin sectionsThe 60- to 70-nm sections cut from the samples in blocksTrimmingProcess of cutting away excess resin to create a block faceUltramicrotomeInstrument used to cut sectionsVitrification/vitreous iceUnordered ice in which samples can be viewed without fix or stainOpen in a separate windowTEM has proven valuable in the analysis of nearly every cellular component, including the cytoskeleton, membrane systems, organelles, and cilia, as well as specialized structures in differentiated cells, such as microvilli and the synaptonemal complex. There is simply no way to visualize the complexity of cells and see cellular structures without TEM. Despite its power, the use of TEM does have limitations. Among the limitations are the relatively small data set of cells that can be imaged in detail, the obligate use of fixed—therefore deceased—cells, and the ever-present potential for fixation and staining artifacts. However, many of these artifacts are well known and have been catalogued (e.g., Bozzola and Russell, 1999 ; Maunsbach and Afzelius, 1999) .A typical TEM experiment consists of two phases: the live-cell experiment, in which a cell type, possibly a mutant, is grown under given conditions for analysis, followed by preparation of the specimen and imaging by TEM. Specimen preparation for conventional TEM is comprehensively reviewed in Hayat (1970) and briefly described here (Figure 1).Open in a separate windowFIGURE 1:A brief flowchart showing the work to be done with different types of sample preparation for conventional electron microscopy (yellow background). The advanced cryo-EM techniques are shown with a blue background. For immuno-EM, the samples can be stained before embedding (pre-embedding staining) or the sections can be stained (post-embedding staining).     

Diminished Susceptibility to Cefoperazone/Sulbactam and Piperacillin/Tazobactam in Enterobacteriaceae Due to Narrow-Spectrum β-Lactamases as Well as Omp Mutation

Cefoperazone/sulbactam (CSL) and piperacillin/tazobactam (TZP) are commonly used in clinical practice in China because of their excellent antimicrobial activity. CSL and TZP-nonsusceptible Enterobacteriaceae are typically resistant to extended-spectrum cephalosporins such as ceftriaxone (CRO). However, 11 nonrepetitive Enterobacteriaceae strains, which were resistant to CSL and TZP yet susceptible to CRO, were collected from January to December 2020. Antibiotic susceptibility tests and whole-genome sequencing were conducted to elucidate the mechanism for this rare phenotype. Antibiotic susceptibility tests showed that all isolates were amoxicillin/clavulanic-acid resistant and sensitive to ceftazidime, cefepime, cefepime/tazobactam, cefepime/zidebactam, ceftazidime/avibactam, and ceftolozane/tazobactam. Whole-genome sequencing revealed three of seven Klebsiella pneumoniae strains harbored bla_SHV-1 only, and four harbored bla_SHV-1 and bla_TEM-1B. Two Escherichia coli strains carried bla_TEM-1B only, while two Klebsiella oxytoca isolates harbored bla_OXY-1-3 and bla_OXY-1-1, respectively. No mutation in the β-lactamase gene and promoter sequence was found. Outer membrane protein (Omp) gene detection revealed that numerous missense mutations of OmpK36 and OmpK37 were found in all strains of K. pneumoniae. Numerous missense mutations of OmpK36 and OmpK35 and OmpK37 deficiency were found in one K. oxytoca strain, and no OmpK gene was found in the other. No Omp mutations were found in E. coli isolates. These results indicated that narrow spectrum β-lactamases, TEM-1, SHV-1, and OXY-1, alone or in combination with Omp mutation, contributed to the resistance to CSL and TZP in CRO-susceptible Enterobacteriaceae.Antibiotic susceptibility tests

A conifer genome spruces up plant phylogenomics

The Norway spruce genome provides key insights into the evolution of plant genomes, leading to testable new hypotheses about conifer, gymnosperm, and vascular plant evolution.In the past year a burst of plant genome sequences have been published, providing enhanced phylogenetic coverage of green plants (Figure ​(Figure1)1) and inclusion of new agricultural, ecological, and evolutionary models. Collectively, these sequences are revealing some extraordinary structural and evolutionary attributes in plant genomes. Perhaps most surprising is the exceptionally high frequency of whole-genome duplication (WGD): nearly every genome that has been analyzed has borne the signature of one or more WGDs, with particularly notable events having occurred in the common ancestors of seed plants, of angiosperms, and of core eudicots (the latter ''WGD'' represents two WGDs in close succession) [1,2]. Given this tendency for plant genomes to duplicate and then return to an essentially diploid genetic system (an example is the cotton genomes, which have accumulated the effects of perhaps 15 WGDs [3]), the conservation of genomes in terms of gene number, chromosomal organization, and gene content is astonishing. From the publication of the first plant genome, Arabidopsis thaliana [4], the number of inferred genes has been between 25,000 and 30,000, with many gene families shared across all land plants, although the number of members and patterns of expansion and contraction vary. Furthermore, conserved synteny has been detected across the genomes of diverse angiosperms, despite WGDs, diploidization, and millions of years of evolution.Open in a separate windowFigure 1Simplified phylogeny of land plants, showing major clades and their component lineages. Asterisks indicate species (or lineage) for which whole-genome sequence (or sequences) is (are) available. Increases and decreases in genome size are shown by arrows.Despite the proliferation of genome sequences available for angiosperms, genome-level data for both ferns (and their relatives, collectively termed monilophytes; Figure ​Figure1)1) and gymnosperms have been conspicuously lacking - until recently, with the publication of the genome sequence of the gymnosperm Norway spruce (Picea abies) [5]. The large genome sizes for both monilophytes and gymnosperms have discouraged attempts at genome sequencing and assembly, whereas the smaller genome size of angiosperms has resulted in more genome sequences being available (Table ​(Table1)1) [6]. Because of this limited phylogenetic sample, our understanding of the timing and phylogenetic positions of WGDs, the core number of plant genes, possible conserved syntenic regions, and patterns of expansion and contraction of gene families across both tracheophytes (vascular plants) and across all land plants is imperfect. This sampling problem is particularly acute in analyses of the genes and genomes of seed plants; many hundreds of genes are present in angiosperms that are not present in mosses or lycophytes, but whether these genes arose in the common ancestor of seed plants or of angiosperms cannot be determined without a gymnosperm genome sequence. The Norway spruce genome therefore offers tremendous power, not only for understanding the structure and evolution of conifer genomes, but also as a reference for interpreting gene and genome evolution in angiosperms.

Table 1

Genome sizes in land plants

Ophthalmic artery chemosurgery for less advanced intraocular retinoblastoma: five year review

Background

Ophthalmic artery chemosurgery (OAC) for retinoblastoma was introduced by us 5 years ago for advanced intraocular retinoblastoma. Because the success was higher than with existing alternatives and systemic side effects limited we have now treated less advanced intraocular retinoblastoma (Reese-Ellsworth (RE) I-III and International Classification Retinoblastoma (ICRB) B and C).

Methodology/Principal Findings

Retrospective review of 5 year experience in eyes with Reese Ellsworth (Reese-Ellsworth (RE) Classification For Intraocular Retinoblastoma GROUP I a. Solitary tumor, less than 4 disc diameters in size, at or behind the equator b. Multiple tumors, none over 4 disc diameters in size, all at or behind the equator GROUP II a. Solitary tumor, less than 4 to 10 disc diameters in size, at or behind the equator b. Multiple tumors, none over 4 to 10 disc diameters in size, all at or behind the equator GROUP III a. Any lesion anterior to the equator b. Solitary tumors larger than 10 disc diameters behind the equator GROUP IV a. Multiple tumors, some larger than 10 disc diameters b. Any lesion extending anteriorly to the ora serrata GROUP V a . Massive tumors involving over half the retina b . Vitreous seeding Open in a separate window

Table 2

International Classification for Retinoblastoma (ICRB) Scheme.

Use of methotrexate therapy is not associated with decreased prevalence of metabolic syndrome

With great interest, we read the article by Toms and colleagues [1] in the previous issue of Arthritis Research & Therapy, in which they assessed prevalences of metabolic syndrome (MetS) in rheumatoid arthritis (RA) patients. Moreover, they identified demographic and clinical factors that may be associated with MetS. Toms and colleagues found prevalences of up to 45% of MetS and demonstrated older age and health status (health assessment questionnaire) to be associated with MetS irrespectively of the definition used. Of most interest, an association between methotrexate (MTX) use and decreased presence of MetS was observed in patients more than 60 years of age. The investigators hypothesized that this may be attributed to a drug-specific effect (and not to an anti-inflammatory effect) either by changing levels of adenosine, which is known to interact with glucose and lipid metabolism, or by an indirect effect mediated through concomitant folic acid administration, thereby decreasing homocysteine levels.Recently, we also examined the prevalence of MetS in (a subgroup of) RA patients in the CARRÉ investigation, a prospective cohort study on prevalent and incident cardiovascular disease and its underlying cardiovascular risk factors [2]. The findings of Toms and colleagues stimulated us to perform additional analyses in our total study population (n = 353).The prevalences of MetS were 35% and 25% (Table ​(Table1)1) according to criteria of National Cholesterol Education Program (NCEP) 2004 and NCEP 2001, respectively. In multivariate backward regression analyses, we found significant associations between body mass index, pulse rate, creatinine levels, hypothyroidism and diabetes mellitus and the presence of MetS independently of the criteria used (Table ​(Table2).2). However, an independent association between single use of MTX or use of MTX in combination with other disease-modifying antirheumatic drugs, on the one hand, and a decreased prevalence of MetS, on the other hand, could not be demonstrated (even in the subgroup of patients over the age of 60).

Table 1

Characteristics of the study population

Hepatitis C Virus (HCV) Sequence Variation Induces an HCV-Specific T-Cell Phenotype Analogous to Spontaneous Resolution

Hepatitis C virus (HCV)-specific CD8⁺ T cells in persistent HCV infection are low in frequency and paradoxically show a phenotype associated with controlled infections, expressing the memory marker CD127. We addressed to what extent this phenotype is dependent on the presence of cognate antigen. We analyzed virus-specific responses in acute and chronic HCV infections and sequenced autologous virus. We show that CD127 expression is associated with decreased antigenic stimulation after either viral clearance or viral variation. Our data indicate that most CD8 T-cell responses in chronic HCV infection do not target the circulating virus and that the appearance of HCV-specific CD127⁺ T cells is driven by viral variation.Hepatitis C virus (HCV) persists in the majority of acutely infected individuals, potentially leading to chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The cellular immune response has been shown to play a significant role in viral control and protection from liver disease. Phenotypic and functional studies of virus-specific T cells have attempted to define the determinants of a successful versus an unsuccessful T-cell response in viral infections (10). So far these studies have failed to identify consistent distinguishing features between a T-cell response that results in self-limiting versus chronic HCV infection; similarly, the impact of viral persistence on HCV-specific memory T-cell formation is poorly understood.Interleukin-7 (IL-7) receptor alpha chain (CD127) is a key molecule associated with the maintenance of memory T-cell populations. Expression of CD127 on CD8 T cells is typically only observed when the respective antigen is controlled and in the presence of significant CD4⁺ T-cell help (9). Accordingly, cells specific for persistent viruses (e.g., HIV, cytomegalovirus [CMV], and Epstein-Barr virus [EBV]) have been shown to express low levels of CD127 (6, 12, 14) and to be dependent on antigen restimulation for their maintenance. In contrast, T cells specific for acute resolving virus infections, such as influenza virus, respiratory syncytial virus (RSV), hepatitis B virus (HBV), and vaccinia virus typically acquire expression of CD127 rapidly with the control of viremia (5, 12, 14). Results for HCV have been inconclusive. The expected increase in CD127 levels in acute resolving but not acute persisting infection has been found, while a substantial proportion of cells with high CD127 expression have been observed in long-established chronic infection (2). We tried to reconcile these observations by studying both subjects with acute and chronic HCV infection and identified the presence of antigen as the determinant of CD127 expression.Using HLA-peptide multimers we analyzed CD8⁺ HCV-specific T-cell responses and CD127 expression levels in acute and chronic HCV infection. We assessed a cohort of 18 chronically infected subjects as well as 9 individuals with previously resolved infection. In addition, we longitudinally studied 9 acutely infected subjects (5 individuals who resolved infection spontaneously and 4 individuals who remain chronically infected) (Tables ​(Tables11 and ​and2).2). Informed consent in writing was obtained from each patient, and the study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki, as reflected in a priori approval from the local institutional review boards. HLA-multimeric complexes were obtained commercially from Proimmune (Oxford, United Kingdom) and Beckman Coulter (CA). The staining and analysis procedure was as described previously (10). Peripheral blood mononuclear cells (PBMCs) were stained with the following antibodies: CD3 from Caltag; CD8, CD27, CCR7, CD127, and CD38 from BD Pharmingen; and PD-1 (kindly provided by Gordon Freeman). Primer sets were designed for different genotypes based on alignments of all available sequences from the public HCV database (http://hcvpub.ibcp.fr). Sequence analysis was performed as previously described (8).

TABLE 1.

Patient information and autologous sequence analysis for patients with chronic and resolved HCV infection

Aluminum induced proteome changes in tomato cotyledons

Cotyledons of tomato seedlings that germinated in a 20 µM AlK(SO₄)₂ solution remained chlorotic while those germinated in an aluminum free medium were normal (green) in color. Previously, we have reported the effect of aluminum toxicity on root proteome in tomato seedlings (Zhou et al.¹). Two dimensional DIGE protein analysis demonstrated that Al stress affected three major processes in the chlorotic cotyledons: antioxidant and detoxification metabolism (induced), glyoxylate and glycolytic processes (enhanced), and the photosynthetic and carbon fixation machinery (suppressed).Key words: aluminum, cotyledons, proteome, tomatoDifferent biochemical processes occur depending on the developmental stages of cotyledons. During early seed germination, before the greening of the cotyledons, glyoxysomes enzymes are very active. Fatty acids are converted to glucose via the gluconeogenesis pathway.^2,3 In greening cotyledons, chloroplast proteins for photosynthesis and leaf peroxisomal enzymes in the glycolate pathway for photorespiration are metabolized.^2–4 Enzymes involved in regulatory mechanisms such as protein kinases, protein phosphatases, and mitochondrial enzymes are highly expressed.^3,5,6The chlorotic cotyledons are similar to other chlorotic counterparts in that both contains lower levels of chlorophyll, thus the photosynthetic activities are not as active. In order to understand the impact of Al on tomato cotyledon development, a comparative proteome analysis was performed using 2D-DIGE following the as previously described procedure.¹ Some proteins accumulated differentially in Al-treated (chlorotic) and untreated cotyledons (Fig. 1). Mass spectrometry of tryptic digestion fragments of the proteins followed by database search has identified some of the differentially expressed proteins (Open in a separate windowFigure 1Image of protein spots generated by Samspot analysis of Al treated and untreated tomato cotyledons proteomes separated on 2D-DIGE.

Table 1

Proteins identified from tomato cotyledons of seeds germinating in Al-solution