Re-evaluation of phytohormone-independent division of tobacco protoplast-derived cells

We have used a [³H] thymidine incorporation assay and microscopic observation in order to reassess recently published data dealing with the response of tobacco protoplasts to phytohormones, lipochitooligosaccharides and peptides ( Harling et al . 1997 ; Hayashi et al . 1992 ; Miklashevichs et al . 1996 ; Miklashevichs et al . 1997 ; Röhrig et al . 1995 ; Röhrig et al . 1996 ; van de Sande et al . 1996 ; Walden et al . 1994 ). These proliferation assays reveal that, in contrast to published data, isolated cells of the investigated mutant plant lines axi159 ( Hayashi et al . 1992 ; Walden et al . 1994 ), axi4/1 ( Harling et al . 1997 ) and cyi1 ( Miklashevichs et al . 1997 ), which were generated by activation T-DNA tagging, were unable to grow in the absence of auxin or cytokinin. Furthermore, lipochitooligosaccharides which play a key role in the induction of nodules on roots of legumes were unable to promote auxin- or cytokinin-independent cell division in tobacco protoplasts as claimed by Röhrig et al . (1995 , 1996 ). The finding of van de Sande et al . (1996 ) that ENOD40 confers tolerance of high auxin concentration to wild-type tobacco protoplasts was also reinvestigated. The results of our investigations show that we were unable to reproduce the proliferation data presented in this study, which were obtained by counting tobacco protoplast-derived cells undergoing division. In total, none of the published data on phytohormone-independent division of tobacco cells could be reproduced.     

Chorio-Retinitis in Porcine Toxoplasmosis

Porcine toxoplasmosis generally occurs as a latent disease in adolescent and adult pigs, but now and then also manifests itself as a fatal congenital disease in piglets. It is known to occur in USA (Farrel et al. 1952), Germany (Becker 1954), Denmark (Momberg-Jørgensen 1956), Mexico (Varela et al. 1956), Japan (Sato et al. 1958), England (Harding et al. 1961) and Sweden (Hansen et al. to be published).     

Predicting genotoxicity of aromatic and heteroaromatic amines using electrotopological state indices

A quantitative structure-activity relationship (QSAR) model relating electrotopological state (E-state) indices and mutagenic potency was previously described by Cash [Mutat. Res. 491 (2001) 31-37] using a data set of 95 aromatic amines published by Debnath et al. [Environ. Mol. Mutagen. 19 (1992) 37-52]. Mutagenic potency was expressed as the number of Salmonella typhimurium TA98 revertants per nmol (LogR). Earlier work on the development of QSARs for the prediction of genotoxicity indicated that numerous methods could be effectively employed to model the same aromatic amines data set, namely, Debnath et al.; Maran et al. [Quant. Struct.-Act. Relat. 18 (1999) 3-10]; Basak et al. [J. Chem. Inf. Comput. Sci. 41 (2001) 671-678]; Gramatica et al. [SAR QSAR Environ. Res. 14 (2003) 237-250]. However, results obtained from external validations of those models revealed that the effective predictivity of the QSARs was well below the potential indicated by internal validation statistics (Debnath et al., Gramatica et al.). The purpose of the current research is to externally validate the model published by Cash using a data set of 29 aromatic amines reported by Glende et al. [Mutat. Res. 498 (2001) 19-37; Mutat. Res. 515 (2002) 15-38] and to further explore the potential utility of using E-state sums for the prediction of mutagenic potency of aromatic amines.     

Estimation of foot joint kinetics in three and four segment foot models using an existing proportionality scheme: Application in paediatric barefoot walking

Recent studies which estimated foot segment kinetic patterns were found to have inconclusive data on one hand, and did not dissociate the kinetics of the chopart and lisfranc joint. The current study aimed therefore at reproducing independent, recently published three-segment foot kinetic data (Study 1) and in a second stage expand the estimation towards a four-segment model (Study 2).Concerning the reproducibility study, two recently published three segment foot models (Bruening et al., 2014; Saraswat et al., 2014) were reproduced and kinetic parameters were incorporated in order to calculate joint moments and powers of paediatric cohorts during gait. Ground reaction forces were measured with an integrated force/pressure plate measurement set-up and a recently published proportionality scheme was applied to determine subarea total ground reaction forces. Regarding Study 2, moments and powers were estimated with respect to the Instituto Ortopedico Rizzoli four-segment model. The proportionality scheme was expanded in this study and the impact of joint centre location on kinetic data was evaluated.Findings related to Study 1 showed in general good agreement with the kinetic data published by Bruening et al. (2014). Contrarily, the peak ankle, midfoot and hallux powers published by Saraswat et al. (2014) are disputed. Findings of Study 2 revealed that the chopart joint encompasses both power absorption and generation, whereas the Lisfranc joint mainly contributes to power generation.The results highlights the necessity for further studies in the field of foot kinetic models and provides a first estimation of the kinetic behaviour of the Lisfranc joint.     

Leg stiffness in human running: Comparison of estimates derived from previously published models to direct kinematic-kinetic measures

It is not presently clear whether mathematical models used to estimate leg stiffness during human running are valid. Therefore, leg stiffness during the braking phase of ground contact of running was calculated directly using synchronous kinematic (high-speed motion analysis) and kinetic (force platform) analysis, and compared to stiffness calculated using four previously published kinetic models. Nineteen well-trained male middle distance runners (age=21.1±4.1yr; VO(2max)=69.5±7.5mlO(2)kg(-1)min(-1)) completed a series of runs of increasing speed from 2.5 to 6.5ms(-1). Leg stiffness was calculated directly from kinetic-kinematic analysis using both vertical and horizontal forces to obtain the resultant force in the line of leg compression (Model 1). Values were also estimated using four previously published mathematical models where only force platform derived and anthropometric measures were required (Models 2-5; Morin et al., 2005, Morin et al., 2011, Blum et al., 2009, Farley et al., 1993, respectively). The greatest statistical similarity between leg stiffness values occurred with Models 1 and 2. The poorest similarity occurred when values from Model 4 were compared with Model 1. Analyses suggest that the poor correlation between Model 1 other models may have resulted from errors in the estimation in change in leg length during the braking phase. Previously published mathematical models did not provide accurate leg stiffness estimates, although Model 2, used by Morin et al. (2005), provided reasonable estimates that could be further improved by the removal of systematic error using a correction factor (K=1.0496K(Model2)).     

New discovery rarely runs smooth: an update on progranulin/TNFR interactions

Progranulin (PGRN) is a growth factor implicated in various pathophysiological processes, including wound healing, inflammation, tumorigenesis, and neurodegeneration. It was previously reported that PGRN binds to tumor necrosis factor receptors (TNFR) and has therapeutic effects in inflammatory arthritis (Tang et. al, in Science 332:478−484, 2011); however, Chen et al. reported their inability to demonstrate the PGRN-TNFR interactions under their own conditions (Chen et. al, in J Neurosci 33:9202−9213, 2013). A letter-to-editor was then published by the original group in response to the Chen et al. paper that discussed the reasons for the latter’s inability to recapitulate the interactions. In addition, the group published follow-up studies that further reinforced and dissected the interactions of PGRNTNFR. Recently, the dispute about the legitimacy of PGRN-TNFR interactions appears to be finally settled with independent confirmations of these interactions in various conditions by numerous laboratories. This review presents a chronological update on the story of PGRN-TNFR interactions, highlighting the independent confirmations of these interactions in various diseases and conditions.     

New Phytologist 140 (1998), 363–383

In the November 1998 issue of New Phytologist , we published the Tansley review 'Gibberellins: regulating genes and germination' by Sian Ritchie and Simon Gilroy ( New Phytol. (1998) 140 , 363–383). Since its publication, it has come to our attention that text associated with Fig. 4 was omitted during production. The correct figure is reprinted here in full.
We apologise to the author and to our readers for this mistake.
Figure 4. Promoter sequences of various genes expressed in the cereal aleurone and shown to be regulated by GA. The position of each sequence is indicated relative to the start codon. Regions identified as being involved in regulation of the genes are highlighted, as are similar regions in other genes. Sites at which protein has been shown to bind are also indicated. ( a ) Barley Amy 32b (Sutcliff et al ., 1993; Whittier et al ., 1987); wheat Amy 2/54 (Huttley et al ., 1992; Rushton et al ., 1992; Rushton et al ., 1995); barley Amy 46 (Khursheed & Rogers, 1988); barley Amy 2/p155 (Knox et al ., 1987); barley aleurain (Whittier et al ., 1987); barley β-glucanase II (Wolf, 1992); wheat cathepsin B-like (Cejudo et al ., 1992); rice ubiquitin-conjugating enzyme (Chen et al ., 1995). ( b ). Wheat Amy 1/18 (Rushton et al ., 1992); barley Amy pHV 19 (Jacobsen & Close, 1991; Gubler & Jacobsen, 1992)/ Amy 1 / 6-4 (Khursheed & Rogers, 1988; Rogers, Lanahan & Rogers 1994); rice OSamy-a / Amy 3c (Ou-Lee et al ., 1988; Sutcliff et al ., 1991; Yu et al ., 1992; Goldman et al ., 1994); rice Amy 3B (Sutcliffe et al ., 1991); rice OSamy-c (Kim et al ., 1992; Kim & Wu, 1992; Tanida et al ., 1994); rice Amy 1A (Huang et al ., 1990; Itoh et al ., 1995).
Figure 4 ( b ). For legend see facing page.     

Connecting mitochondria and innate immunity

Viral infection results in the activation of multiple signaling pathways, but how these pathways are coordinated remains a mystery. Two studies, one published in this issue of Cell (Seth et al., 2005) and the other in Molecular Cell (Xu et al., 2005), identify a new intracellular signaling protein that is required for activating type I interferon expression in response to viral infection. In addition,Seth et al. (2005) show that the function of this protein, which they call MAVS, requires that it be localized to the mitochondria. This observation establishes an unexpected link between innate immunity and an organelle with evolutionary origins in aerobic bacteria.     

Correction to: Food conditions,competitive regime,and female social relationships in Japanese macaques: within-population variation on Yakushima

Primates - In our published paper (Hanya et al. 2008), we found an error in a figure described in the     

Scientific data laundering: Chimeric mitogenomes of a sparrowhawk and a nightjar covered-up by forged phylogenies

In 2017, Gang Liu and colleagues published a paper in this journal in which they described the first mitochondrial genome of Japanese Sparrowhawk Accipiter gularis (Aves, Accipitriformes). The paper included two phylogenies (one based on full mitogenomes, the other on mitochondrial 12S/16S rRNA sequences) that placed this species among the goshawks and sparrowhawks (genus Accipiter). These phylogenies also included a previously published mitogenome of Grey Nightjar Caprimulgus indicus. Here, we show that the published mitogenome of A. gularis is a chimera of three species (a sparrowhawk, a buzzard and a dove), and that the published mitogenome of C. indicus is a chimera of two owl species. Phylogenetic re-analysis showed substantial differences from those published by Liu et al. (2017): the A. gularis sequence was placed among Streptopelia doves in the 12S/16S rRNA tree, and the C. indicus sequence was placed among Otus owls in the mitogenomic and mitochondrial 12S/16S rRNA trees. The phylogenies in Liu et al. (2017) showed several other peculiarities: (i) the inclusion of Javan Hawk-eagle Nisaetus bartelsi in the mitogenome tree (whereas no mitogenome is available of this species and no such sequence has been described in the literature), (ii) reciprocal monophyly of the genera Buteo, Leucopternis and Buteogallus (whereas multiple previous studies have shown these to be para- or polyphyletic), and (iii) the placement of Black-chested Buzzard Eagle Geranoaetus melanoleucus and Crane Hawk ‘Geranoaetus’ (=Geranospiza) caerulescens as sister species (whereas all previous studies have shown these to be distantly related). Close examination of the figures in Liu et al. (2017) revealed that both phylogenies have been manually prepared or modified. The evidence indicates that Liu et al. (2017) published phylogenies that were not based on existing data but were fabricated to reflect preconceived ideas about phylogenetic relationships. The phylogenies published by Liu et al. (2017) give the impression that the mitogenomic sequence described in their paper (A. gularis) and another one (C. indicus) described by Zhao et al. (2016) are authentic and correctly identified, whereas in reality these sequences are highly problematic chimeras. The term ‘scientific data laundering’ is proposed for the practice of hiding poor or erroneous research data with fabricated or falsified figures.     

Clonal plants: beyond the patterns—ecological and evolutionary dynamics of asexual reproduction

More than 25 years have passed since publication of the first comprehensive multi-authored landmark volume on the population biology and evolution of clonal organisms (Jackson et al. 1985). Since then, no less than eight symposium volumes or special issues have appeared in scientific journals reporting on advances in the field of clonal plant research, indicating that the study of clonal organisms has remained an important topic in ecological research. The three most recent overviews were published in special issues of this journal (Stuefer et al. 2000; Tolvanen et al. 2004; Sammul et al. 2008), and these are now supplemented with a fourth special issue of Evolutionary Ecology. The articles published here reflect some of the most important contributions to a workshop on clonal plant biology held in Leuven (Belgium) in July 2009 and they illustrate some major advances that have been made over the last few years. In the following paragraphs, we first summarize some representative contributions to the current issue, and second, we put forward some personal ideas about promising and underexplored research lines in clonal plant research.     

组织型纤溶酶原激活剂（t－PA）cDNA序列的测定

已经从ｍｅｌａｎｏｍａ细胞系中成功地获得了人组织型纤溶酶原激活剂（ｔ－ＰＡ）ｃＤＮＡ,在此基础上用双脱氧终止法测定了ｔ－ＰＡｃＤＮＡ编码区全序列及３′非编码区部分序列,并发现与Ｐｅｎｎｉｃａ等发表的ｔ－ＰＡｃＤＮＡ序列相比,有两处差异,其一是第１７２５位核苷酸残基为Ｃ而非Ａ,并使此处序列与Ｐｅｎｎｉｃａ序列相比新产生一个ＳｔｙＩ切点,但由于差异发生在密码子第三位,没有引起编码的氨基酸变化;其二是第１７７７位核苷酸残基（终止密码子后第４位核苷酸残基）为Ｔ而非Ｇ,使与终止密码子相隔３个核苷酸残基处产生了一个新的ＴＧＡ,与Ｐｅｎｎｉｃａ序列相比此处的ＢｓｔＮＩ切点也消失了。     

Dynamically forecasting network performance using the Network Weather Service

The Network Weather Service is a generalizable and extensible facility designed to provide dynamic resource performance forecasts in metacomputing environments. In this paper, we outline its design and detail the predictive performance of the forecasts it generates. While the forecasting methods are general, we focus on their ability to predict the TCP/IP end-to-end throughput and latency that is attainable by an application using systems located at different sites. Such network forecasts are needed both to support scheduling (Berman et al., 1996) and, by the metacomputing software infrastructure, to develop quality-of-service guarantees (DeFanti et al., to appear; Grimshaw et al., 1994). This revised version was published online in July 2006 with corrections to the Cover Date.     

Face Recognition and Visual Search Strategies in Autism Spectrum Disorders: Amending and Extending a Recent Review by Weigelt et al.

The purpose of this review was to build upon a recent review by Weigelt et al. which examined visual search strategies and face identification between individuals with autism spectrum disorders (ASD) and typically developing peers. Seven databases, CINAHL Plus, EMBASE, ERIC, Medline, Proquest, PsychInfo and PubMed were used to locate published scientific studies matching our inclusion criteria. A total of 28 articles not included in Weigelt et al. met criteria for inclusion into this systematic review. Of these 28 studies, 16 were available and met criteria at the time of the previous review, but were mistakenly excluded; and twelve were recently published. Weigelt et al. found quantitative, but not qualitative, differences in face identification in individuals with ASD. In contrast, the current systematic review found both qualitative and quantitative differences in face identification between individuals with and without ASD. There is a large inconsistency in findings across the eye tracking and neurobiological studies reviewed. Recommendations for future research in face recognition in ASD were discussed.     

Young haematopoietic stem cells are picky eaters

In a recent study published in Nature,Dong et al.describe how haematopoietic stem cells(HSCs)rely on chaperone-mediated autophagy(CMA),a form of highly selectiv...     

Passing the message on: inheritance of epigenetic traits

Epigenetic modifiers play an important role in genome organization, stability and the control of gene expression. Three research groups that are exploring the transfer of epigenetic information between generations have recently published papers. Mary Alleman et al. have shown that RNA-directed chromatin changes mediate paramutation in maize, and Minoo Rassoulzadegan et al. have demonstrated that RNA also plays a role in paramutation in mice. A new aspect of epigenetic regulation has been revealed by Jean Molinier et al. - they have demonstrated that the memory of exposure to stress is transferred through several generations.