Targeted Gene Knockouts Reveal Overlapping Functions of the Five Physcomitrella patens FtsZ Isoforms in Chloroplast Division,Chloroplast Shaping,Cell Patterning,Plant Development,and Gravity Sensing

Chloroplasts and bacterial cells divide by binary fission. The key protein in this constriction division is FtsZ, a self-assembling GTPase similar to eukaryotic tubulin. In prokaryotes, FtsZ is almost always encoded by a single gene, whereas plants harbor several nuclear-encoded FtsZ homologs. In seed plants, these proteins group in two families and all are exclusively imported into plastids. In contrast, the basal land plant Physcomitrella patens, a moss, encodes a third FtsZ family with one member. This protein is dually targeted to the plastids and to the cytosol. Here, we report on the targeted gene disruption of all ftsZ genes in R patens. Subsequent analysis of single and double knockout mutants revealed a complex interaction of the different FtsZ isoforms not only in plastid division, but also in chloroplast shaping, cell patterning, plant development, and gravity sensing. These results support the concept of a plastoskeleton and its functional integration into the cytoskeleton, at least in the moss R patens.     

Clues to the signals for chloroplast photo-relocation from the lifetimes of accumulation and avoidance responses

Chloroplast photo-relocation movement is crucial for plant survival; however, the mechanism of this phenomenon is still poorly understood. Especially, the signal that goes from photoreceptor to chloroplast is unknown, although the photoreceptors(phototropin 1 and 2) have been identified and an actin structure(chloroplast actin filaments) has been characterized that is specific for chloroplast movement. Here,in gametophytes of the fern Adiantum capillus-veneris,gametophores of the moss Physcomiterella patens, and leaves of the seed plant Arabidopsis thaliana, we sought to characterize the signaling system by measuring the lifetime of the induced response. Chloroplast movements were induced by microbeam irradiation with high-intensity blue light and recorded. The lifetime of the avoidance state was measured as a lag time between switching off the beam and the loss of avoidance behavior, and that of the accumulation state was measured as the duration of accumulation behavior following the extinction of the beam. The lifetime for the avoidance response state is approximately 3–4 min and that for the accumulation response is 19–28 min. These data suggest that the two responses are based on distinct signals.     

Heterologous expression of Hp BHY and Cr BKT increases heat tolerance in Physcomitrella patens

Heat stress can restrict plant growth,development,and crop yield.As essential plant antioxidants,carotenoids play significant roles in plant stress resistance.b-carotene hydroxylase(BHY)and b-carotene ketolase(BKT),which catalyze the conversions of b-carotene to zeaxanthin and b-carotene to canthaxanthin,respectively,are key enzymes in the carotenoid biosynthetic pathway,but little is known about their potential functions in stress resistance.Here,we investigated the roles of b-carotene hydroxylase and b-carotene ketolase during heat stress in Physcomitrella patens through expressing a b-carotene ketolase gene from Chlamydomonas reinhardtii(Cr BKT)and a b-carotene hydroxylase gene from Haematococcus pluvialis(Hp BHY)in the moss P.patens.In transgenic moss expressing these genes,carotenoids content increased(especially lutein content),and heat stress tolerance increased,with reduced leafy tissue necrosis.To investigate the mechanism of this heat stress resistance,we measured various physiological indicators and found a lower malondialdehyde level,higher peroxidase and superoxide dismutase activities,and higher endogenous abscisic acid and salicylate content in the transgenic plants in response to high-temperature stress.These results demonstrate that Cr BKT and Hp BHY increase plant heat stress resistance through the antioxidant and damage repair metabolism,which is related to abscisic acid and salicylate signaling.     

Thoughts about cancer stem cells in solid tumors

Cancer chemotherapy efficacy is frequently impaired by either intrinsic or acquired tumor resistance.A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells.In recent years,the cancer stem cell(CSC) theory has changed the classical view of tumor growth and therefore the therapeutic perspective.Overcoming intrinsic and acquired resistance of cancer stem/progenitor cells to current clinical treatments represents a major challenge in treating and curing the most aggressive and metastatic cancers.On the other hand,the identification of CSCs in vivo and in vitro relies on specific surface markers that should allow the sorting cancer cells into phenotypically distinct subpopulations.In the present review,recent papers published on CSCs in solid tumors(breast,prostate,brain and melanoma) are discussed,highlighting critical points such as the choice of markers to sort CSCs and mouse models to demonstrate that CSCs are able to replicate the original tumor.A discussion of the possible role of aldehyde dehydrogenase and CXCR6 biomarkers as signaling molecules in CSCs and normal stem cells is also discussed.The author believes that efforts have to be made to investigate the functional and biological properties of putative CSCs in cancer.Developing diagnostic/prognostic tools to follow cancer development is also a challenge.In this connection it would be useful to develop a multidisciplinary approach combining mathematics,physics and biology which merges experimental approaches and theory.Biological models alone are probably unable to resolve the problem completely.     

Manipulating mRNA splicing by base editing in plants

Precursor-mRNAs(pre-mRNA) can be processed into one or more mature m RNA isoforms through constitutive or alternative splicing pathways. Constitutive splicing of pre-mRNA plays critical roles in gene expressional regulation, such as intronmediated enhancement(IME), whereas alternative splicing(AS) dramatically increases the protein diversity and gene functional regulation. However, the unavailability of mutants for individual spliced isoforms in plants has been a major limitation in studying the function of mRNA splicing. Here, we describe an efficient tool for manipulating the splicing of plant genes. Using a Cas9-directed base editor, we converted the 5′ splice sites in four Arabidopsis genes from the activated GT form to the inactive AT form. Silencing the AS of HAB 1.1(encoding a type 2 C phosphatase) validated its function in abscisic acid signaling, while perturbing the AS of RS31 A revealed its functional involvement in plant response to genotoxic treatment for the first time. Lastly,altering the constitutive splicing of Act2 via base editing facilitated the analysis of IME. This strategy provides an efficient tool for investigating the function and regulation of gene splicing in plants and other eukaryotes.     

Index selection on seed traits under direct, cytoplasmic and maternal effects in multiple environments

Crop seeds are important sources of protein, oil, and carbohydrates for food, animal feeds, and industrial products. Recently, much attention has been paid to quality and functional properties of crop seeds. However, seed traits possess some distinct genetic characteristics in comparison with plant traits, which increase the difficulty of genetically improving these traits. In this study, diallel analysis for seed models with genotype by environment interaction （GE） effect was applied to estimate the variance-covariance components of seed traits. Mixed linear model approaches were used to estimate the genetic covariances between pair-wise seed and plant traits. The breeding values （BV） were divided into two categories for the seed models. The first category of BV was defined as the combination of direct additive, cytoplasmic, and maternal additive effects, which should be utilized for selecting stable cultivars over multi-environments. The three genetic effects, together with their GE interaction, were included in the second category of BV for selecting special lines to be grown in specific ecosystems. Accordingly, two types of selection indices for seed traits, i.e., general selection index and interaction selection index, were developed and constructed on the first and the second category BV, respectively. These proposed selection indices can be applied to solve the difficult task of simultaneously improving multiple seed traits in various environments. Data of crop seeds with regard to four seed traits and four yield traits based on the modified diallel crosses in Upland cotton （Gossypium hirsutum L.） were used as an example for demonstrating the proposed methodology.     

Widely predicting specific protein functions based on protein-protein interaction data and gene expression profile

GESTs (gene expression similarity and taxonomy similarity), a gene functional prediction approach previously proposed by us, is based on gene expression similarity and concept similarity of functional classes defined in Gene Ontology (GO). In this paper, we extend this method to protein-protein interac-tion data by introducing several methods to filter the neighbors in protein interaction networks for a protein of unknown function(s). Unlike other conventional methods, the proposed approach automati-cally selects the most appropriate functional classes as specific as possible during the learning proc-ess, and calls on genes annotated to nearby classes to support the predictions to some small-sized specific classes in GO. Based on the yeast protein-protein interaction information from MIPS and a dataset of gene expression profiles, we assess the performances of our approach for predicting protein functions to “biology process” by three measures particularly designed for functional classes organ-ized in GO. Results show that our method is powerful for widely predicting gene functions with very specific functional terms. Based on the GO database published in December 2004, we predict some proteins whose functions were unknown at that time, and some of the predictions have been confirmed by the new SGD annotation data published in April, 2006.     

Cysteine and Cysteine-Related SignalingPathways in Arabidopsis thaliana

Cysteine occupies a central position in plant metabolism because it is a reduced sulfur donor moleculeinvolved in the synthesis of essential biomolecules and defense compounds. Moreover, cysteine per se and its deriva-tive molecules play roles in the redox signaling of processes occurring in various cellular compartments. Cysteine issynthesized during the sulfate assimilation pathway via the incorporation of sulfide to O-acetylserine, catalyzed byO-acetylserine（thiol）lyase （OASTL）. Plant cells contain OASTLs in the mitochondria, chloroplasts, and cytosol, resultingin a complex array of isoforms and subcellular cysteine pools, in recent years, significant progress has been made inArabidopsis, in determining the specific roles of the OASTLs and the metabolites produced by them. Thus, the dis-covery of novel enzymatic activities of the less-abundant, like DES1 with L-cysteine desulfhydrase activity and SCSwith S-sulfocysteine synthase activity, has provided new perspectives on their roles, besides their metabolic functions.Thereby, the research has been demonstrated that cytosolic sulfide and chloroplastic S-sulfocysteine act as signalingmolecules regulating autophagy and protecting the photosystems, respectively. In the cytosol, cysteine plays an essentialrole in plant immunity; in the mitochondria, this molecule plays a central role in the detoxification of cyanide, which isessential for root hair development and plant responses to pathogens.     

Dynamic data replacement and adaptive scheduling policies in spark

Improper data replacement and inappropriate selection of job scheduling policy are important reasons for the degradation of Spark system operation speed, which directly causes the performance degradation of Spark parallel computing. In this paper, we analyze the existing caching mechanism of Spark and find that there is still more room for optimization of the existing caching policy. For the task structure analysis, the key information of Spark tasks is taken out to obtain the data and memory usage during the task runtime, and based on this, an RDD weight calculation method is proposed, which integrates various factors affecting the RDD usage and establishes an RDD weight model. Based on this model, a minimum weight replacement algorithm based on RDD structure analyzing is proposed. The algorithm ensure that the relatively more valuable data in the data replacement process can be cached into memory. In addition, the default job scheduling algorithm of the Spark framework considers a single factor, which cannot form effective scheduling for jobs and causes a waste of cluster resources. In this paper, an adaptive job scheduling policy based on job classification is proposed to solve the above problem. The policy can classify job types and schedule resources more effectively for different types of jobs. The experimental results show that the proposed dynamic data replacement algorithm effectively improves Spark's memory utilization. The proposed job classification-based adaptive job scheduling algorithm effectively improves the system resource utilization and shortens the job completion time.

     

Reconstitution de la végétation et du paléoclimat à partir de charbons de bois prélevés sur les sites du Paléolithique dans la région de Jungwon en Corée

Hundreds samples of the charcoals and waterlogged woods excavated from three late Paleolithic sites (Suyanggae, Gunang-gul and Sorori) in the Jungwon Region in Korea were analyzed to reconstruct the vegetation and paleoclimate in the region. Analyzed charcoal samples from the Suyanggae site show that the climate was cold in the lower part and it became more warm and dry in the upper part. From the Gunang-gul site, only Picea spp. was identified, indicating cool climates. From the Sorori site, two species were found; Alnus spp. (95%) and Ulmus spp. (5%). No conifers were discovered. The species composition indicates that the climate condition of central Korean peninsula around 8,800 BP was little cooler and wetter condition.     

« Flûte » et pointes de la Grosse Badlhöhle, Autriche

The Grosse Badlhöhle (Austria, Steiermark) is the origin of one of the most perfect bone points of the early Aurignacian and one of the best perforated femurs of the same period, which can be regarded as musical instruments. Two other fragments of points raise intriguing questions on the first Homo sapiens sapiens which cannot be solved today but will contribute to future research. A review on the debate of Palaeolithic flutes will follow with experimental proofs of boring artificial holes with high quality pictures on the blow-hole and the lack of gnawing traces on the opposite face. The musical possibility of an instrument with only one hole is discussed with ethnographic analogies. Hafting, optimal conditions of strength and possible use of arrows will close the discussion on the Badlhöhle bone artefacts.     

Comparaison de l'expression de certains caractères crâniens sur les hominidés chinois du Pléistocène récent et de l'Holocène (grotte supérieure de Zhoukoudian, sites de Longxian et de Yanqing)

The human remains recovered from “Grotte supérieure de Zhoukoudian” are the best-preserved Late Pleistocene human fossils in East Asia. For decades, as the representative of the Late Pleistocene human in East Asia, the Upper Cave skulls have been playing important role in the research of origins of modern Mongoloids and American Indians. With the advance of the origin and evolution of modern humans, more attention has been paid to the details and the mechanisms for the late Pleistocene human evolution and the formation of modern human populations. Both the origin and diversification of modern humans have been stressed. Some studies further trigger the debaters on the Upper Cave Man concerning its evolutionary level and its role in the formation of modern human populations in East Asia. To further explore these problems, we examined and compared 12 non-metric features on the 3 Late Pleistocene Upper Cave skulls and 162 Holocene individuals earthed from two archaeological sites of North China (Longxian and Yanqing). Our results indicate that 8 on the 12 features have different expression patterns between Upper Cave Man and recent Chinese leading the authors to believe that more primitive expressions appeared on the Upper Cave Man than on recent Chinese populations. Based on these findings, some problems on the intragroup variation in Late Pleistocene and Holocene populations are discussed.     

Conception et exécution de bases de données intégrées pour l'analyse des rapports spatiotemporels des artefacts du Paléolithique

The archaeologists excavate the historic site and analyze data from the excavation site. Therefore, they study about the past affairs and circumstances unknown to the world. These data are composed of stones, plants, bones and geological features, which are stored in separate files according to the fields of study. It is important to mention that this information become the first step toward the solution of some hypothesis in Archaeology. Therefore, we need the system that can not only support integrated environment to find clues of the past, but also manage existing artifact data systematically and grasp relationships among the data. In this paper, we modeled the time, which is used in archaeology and geology, and built an entity relationship database to store Paleolithic data excavated in Jungwon region site of the Republic of Korea as one resource, which seem to give a base for integrated research and relationships in archaeology. In addition, we developed the Graphic User Interface that allows various users to connect to the established system through the web.     

L'hominidé du Pléistocène supérieur en Corée

Since the middle of 1970s, one rock-shelter, six caves and one open archaeological site have yielded several hominid fossils. Among them, fossils from Yonggok, Mandal, Sangsi and Hungsu cave sites are useful to reconstruct the general shape of the Upper Pleistocene Hominids in Korea. The main study of this paper is to focus on the reconstruction of the general shape of the upper Pleistocene hominids, and to examine the cause of cranial changes from the late upper Paleolithic to Mesolithic period in Korea. Biomechanical principles are also applied to reconstruct the social activity of the upper Paleolithic man in Korea. In addition, it is assumed that main proponent of Paleolithic cultures in Korea might be Homo sapiens rather than any other species. Based on the anatomical characteristics of skull, the axillary border of the scapular and the midshaft of the femur, general appearance of Homo sapiens during the Pleistocene in Korea could be reconstructed.     

La stratigraphie du Pléistocène supérieur et le Paléolithique en Corée

In Korea, Quaternary deposits are characterized by marine and fluvial terrace deposits, commonly found in the coastal areas and at the sides of river valleys. The major terraces are classified into 5 different levels, i.e., alluvial plain (3-5 m asl), lower terrace (10-25 m asl), middle terrace (33-50 m asl), high terrace (55-85 m asl), and highest terrace (90-160 m asl). They were formed by the repetition of sedimentation and erosion due to sea level fluctuation and uplifting along the coastal areas during Quaternary period. The formation age of the lower marine terraces at the level of 10-20 m is interpreted to be the last interglacial (75-125 Ka, MIS = 5a-5e). The middle coastal terrace gravels distributed at the level of about 33-45 m above mean sea level and are to be formed before the last interglacial. Above coastal terrace deposits, slope deposits and paleosol layers are overlain and freezing and thawing crackings were developed in them. Major prehistory archaeological sites in the coastal areas are found in the slope deposits formed during last glaciations. The upper parts of the slope deposits are typified by paleosol layers with typical frost cracks (soil wedges) and frangipanes. As geochronological bases for subdividing Paleolithic cultures, two typical paleosol layers are useful because they are mostly found and imprinted with several horizons of frost cracks or soil wedges. The uppermost crack structures were formed under the boreal-periglacial climatic regime during the last glacial period of extremely cold-dry climate in Korea. The upper pedogenetic sediments containing frost cracks or soil wedges were formed between 24 and 17 Ka in many Paleolithic profiles. The lowermost paleosol layer with frost cracks (soil wedge), strongly attacked into hillslope sediments or last interglacial saprolite layers on the weathered basement rocks, were detected at least as old as 59-74,000 Ka. Lastly upper Paleolithic cultural layers were found in the young fluvial deposits, which had been formed since the Last Glacial Maximum (LGM). Some of them were particularly continued as late as the Pleistocene-Holocene Transition Period.     

Le groupe des « bisons adossés » de Lascaux. Étude de la technique de l'artiste par analyse des pigments

The painting matter of the “back to back bison's panel” of Lascaux was examined and analysed by electron microscopy in order to understand the know-how of Magdalenian artists. The observation of several samples coming from specific areas of the two bisons give an access to the nature of the used pigments, to the preparation mode used to obtain various colours and also to the application mode. Thanks to this physicochemical approach, we can make hypotheses about the mind and the gestures of the artists.     

Évolution de la préhension chez les primates humains et non humains : la précision et l'utilisation d'outils revisitées

The term “precision”, involving the contact between the tips of thumb and the index is generally attributed to humans, tool use and associated with morphological criteria. Identified in fossils, those criteria are used to assert that they manipulated tools. Observations of 69 individuals belonging to Catarrhines and Platyrrhines allowed us to quantify surfaces of fingers used during simple tasks of grasping both small and large objects, as well as during complex tasks of proto-tool and tool use. We concluded that precision grasping is not peculiar to humans and that it is not systematically linked to tool use. These results allowed us to discuss morphological traits used till now to deduce precision and tool use from the fossils. Besides, our analyses let appear a recurrent proximity between the capuchins and the humans, species distant in a phylogenetic point of view, suggesting the possible existence of functions and close behaviours in spite of great genetic distinctions.