Terpenoid precursors of strigol as seed germination stimulants of broomrape (Orobanche ramosa) and witchweed (Striga asiatica)

Strigol and some of its synthetic precursors and analogs are known to be germination stimulants for broomrape (Orobanche ramosa) and witchweed (Striga asiatica). Fifteen synthetic terpenoids, similar in structure to one of the four rings of the strigol molecule, were evaluated in two bioassays as seed germination stimulants with broomrape, and nine were found to be active. Five of the more active compounds contained ester groups. Whereas the study was intended primarily to evaluate forced germination of broomrape by aqueous solutions, the results are almost qualitatively identical for broomrape and witchweed. Monocyclic compounds with chemical structures similar to two of the rings of strigol have now been shown to possess significant bioactivity as germination stimulants.Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply its approval to the exclusion of other products or vendors that may also be suitable.     

Deep learning for computational biology

Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.     

Water masses in the Bransfield Strait and adjacent seas,austral summer 2013

The Bransfield Strait is a semi-enclosed sea located in the northern part of the West Antarctic Peninsula region, which is subject to strong climatic changes. The bathymetry is complex and comprises three basins that are separated from each other by shallow sills. Oceanographic measurements of the Bransfield Strait region are available since the first half of the twentieth century. In this study, hydrographic data from the ANT-XXIX/3 expedition of RV Polarstern in 2013 are presented to describe the actual physical state of the art, particularly for biological work done during that cruise. The general hydrographic situation of the Bransfield Strait in 2013 is found to be similar to observations from the early twentieth century. The Bransfield Strait’s water masses are modified versions of the water masses from the adjacent seas. The different water masses within the Bransfield Strait are separated by two fronts, the so-called Bransfield and Peninsula Front. While the Bransfield Front is most pronounced in the central and southwestern Bransfield Strait, the Peninsula Front can be identified from the northeastern to the central part of the study domain. Based on an analysis of water mass properties around the Antarctic Peninsula and close to the Antarctic Sound, a notable inflow of Shelf Water from the Weddell Sea through the Antarctic Sound appears unlikely.     

Changes in DNA supertwist as a response of Bacillus subtilis towards different kinds of stress

Abstract The silent parD ( kis/kid ) stability operon of plasmid R1 is normally repressed by the co-ordinated action of the Kis and Kid proteins. In this report it is shown that a mutation in repA , the gene of the plasmid replication protein, that reduces two-fold the copy number of the plasmid, leads to the derepression of the parD system. This derepression can be prevented by a suppressor mutation in copB, a copy number control gene of plasmid R1, that increases the efficiency of replication of the repA mutant. Derepression of the wild-type parD system leads to high plasmid stability. These data show the activation of a plasmid stability operon by a mutation that reduces the efficiency of wild-type plasmid replication.     

Hypoxia. Hypoxia in the pathogenesis of systemic sclerosis

Autoimmunity, microangiopathy and tissue fibrosis are hallmarks of systemic sclerosis (SSc). Vascular alterations and reduced capillary density decrease blood flow and impair tissue oxygenation in SSc. Oxygen supply is further reduced by accumulation of extracellular matrix (ECM), which increases diffusion distances from blood vessels to cells. Therefore, severe hypoxia is a characteristic feature of SSc and might contribute directly to the progression of the disease. Hypoxia stimulates the production of ECM proteins by SSc fibroblasts in a transforming growth factor-β-dependent manner. The induction of ECM proteins by hypoxia is mediated via hypoxia-inducible factor-1α-dependent and -independent pathways. Hypoxia may also aggravate vascular disease in SSc by perturbing vascular endothelial growth factor (VEGF) receptor signalling. Hypoxia is a potent inducer of VEGF and may cause chronic VEGF over-expression in SSc. Uncontrolled over-expression of VEGF has been shown to have deleterious effects on angiogenesis because it leads to the formation of chaotic vessels with decreased blood flow. Altogether, hypoxia might play a central role in pathogenesis of SSc by augmenting vascular disease and tissue fibrosis.     

Genetic variation in nine Shorea species (Dipterocarpaceae) in Indonesia revealed by AFLPs

Shorea is the largest and most important genus of the Dipterocarpaceae. The genetic diversity and structure of nine Shorea species from two different locations, namely Nanjak Makmur in Sumatra and Sumalindo in Borneo, were evaluated using amplified fragment length polymorphism (AFLP) markers. A total of 274 trees were investigated at 85 polymorphic AFLP loci. Levels of genetic diversity of these species ranged from  = 0.100 for S. acuminata to  = 0.165 for S. blumutensis. The population of rare species S. blumutensis possessed the highest genetic diversity suggesting that geographically restricted species can have levels of genetic variation comparable to closely related widespread common congeners. Analyses of molecular variance revealed that the genetic variation was mainly found among species in both locations (57.7% in Sumatra; 56.3% in Borneo). The unweighted pairgroup method using arithmetic averages dendrogram of all samples revealed an almost complete separation of species. Thus, AFLP markers proved appropriate for phylogenetic studies of Shorea species. Specific markers have been detected showing high-frequency differences among species and between regions within species. Sequence information of these markers can be used to develop specific polymerase chain reaction markers for wood identification. The possibility of interspecific hybridization was discussed.     

Leaf traits from stomata to morphology are associated with climatic and edaphic variables for dominant tropical forest evergreen oaks

热带森林优势种青冈叶片气孔、解剖和形态性状与气候、土壤因子的关联 了解优势树种叶片多水平的功能性状沿海拔梯度的变化及其内在关联,有助于预测优势种应对气候变化的响应与适应。本文研究了青冈属树种叶片气孔、解剖和形态性状沿海拔梯度的变化及其与环境调控因子的关联,探究了其生态策略是否随海拔发生改变。在海南尖峰岭热带森林,沿海拔梯度(400–1400 m)采集了6种常绿青冈：竹叶青冈(Cyclobalanopsis bambusaefolia)、雷公青冈(C. hui)、托盘青冈 (C. patelliformis)、饭甄青冈(C. fleuryi)、吊罗山青冈(C. tiaoloshanica)和亮叶青冈(C. phanera)叶片,用于气孔、解剖和形态性状的测定。研究结果表明,随海拔升高,青冈树种叶片气孔密度、气孔孔隙度指数和叶面积显著增加,但海绵组织厚度比和干物质含量则显着降低。叶片气孔、解剖和形态性状沿海拔梯 度的变化主要受年均温、年降水量和土壤pH 值调控。在低海拔和高海拔处,青冈属采取“耐受”和“竞 争”策略,而在中海拔处,则是“竞争”策略。土壤磷含量和土壤pH 值随海拔的变化可能是驱动其生态 策略转变的主要原因。该结果揭示,热带森林优势树种青冈可通过从气孔细胞-组织解剖结构-叶片水平功能性状的改变来响应环境变化。     

An ecological paradox: More woodland predators and less artificial nest predation in landscapes colonized by noisy miners

Many passerine bird populations, particularly those that have open‐cup nests, are in decline in agricultural landscapes. Current theory suggests that an increase in habitat generalist predators in response to landscape change is partially responsible for these declines. However, empirical tests have failed to reach a consensus on how and through what mechanisms landscape change affects nest predation. We tested one hypothesis, the Additive Predation Model, with an artificial nest experiment in fragmented landscapes in southern Queensland, Australia. We employed structural equation modelling of the influence of the relative density of woodland and habitat generalist predators and landscape features at the nest, site, patch and landscape scales on the probability of nest predation. We found little support for the Additive Predation Model, with no significant influence of the density of woodland predators on the probability of nest predation, although landscape features at different spatial scales were important. Within woodlands fragmented by agriculture in eastern Australia, the presence of noisy miner colonies appears to influence ecological processes important for nest predation such that the Additive Predation Model does not hold. In the absence of colonies of the aggressive native bird, the noisy miner, the influence of woodland predators on the risk of artificial nest predation was low compared with that of habitat generalist predators. Outside noisy miner colonies, we found significant edge effects with greater predation rates for artificial nests within woodland patches located closer to the agricultural matrix. Furthermore, the density of habitat generalist predators increased with the extent of irrigated land‐use, suggesting that in the absence of noisy miner colonies, nest predation increases with land‐use intensity at the landscape scale.     

Physiological history may mask the inherent inducible desiccation tolerance strategy of the desert moss Crossidium crassinerve

Shoots of bryophytes collected in the desiccated state from the field are likely to be hardened to desiccation tolerance (DT) to varying degrees. To account for this, most studies on DT include a relatively short deacclimation period. However, no study has experimentally determined the appropriate deacclimation time for any bryophyte species. Our purposes are to (i) determine if ‘field effects’ are biologically relevant to DT studies and how long a deacclimation period is required to remove them; and (ii) utilise field versus cultured shoot responses within the context of a deacclimation period to elucidate the ecological strategy of DT. Our hypothesis (based on an extensive literature on DT) is that a deacclimation period from 24 to 72 h should be sufficient to eliminate historical stress effects on the physiology of the shoots and allow an accurate determination of the inherent ecological DT strategy (constitutive or inducible). We determined, however, using chlorophyll fluorescence and visual estimates of shoot damage, that field‐collected shoots of the desert moss Crossidium crassinerve required an experimental deacclimation period of >7 days before field effects were removed, and revealed an ecological DT strategy of inducible DT. If the deacclimation period was <6 days, the shoot response conformed to an ecological strategy of constitutive protection. Thus the presence of field effects can obscure the ecological strategy of desiccation tolerance exhibited by the species, and this translates into a need to re‐evaluate previous mechanistic and ecological studies of desiccation tolerance in plants.     

Ovine Model for Critical-Size Tibial Segmental Defects

A segmental tibial defect model in a large animal can provide a basis for testing materials and techniques for use in nonunions and severe trauma. This study reports the rationale behind establishing such a model and its design and conclusions. After ethics approval of the study, aged ewes (older than 5 y; n = 12) were enrolled. A 5-cm mid diaphyseal osteoperiosteal defect was made in the left tibia and was stabilized by using an 8-mm stainless-steel cross-locked intramedullary nail. Sheep were euthanized at 12 wk after surgery and evaluated by using radiography, microCT, and soft-tissue histology techniques. Radiology confirmed a lack of hard tissue callus bridging across the defect. Volumetric analysis based on microCT showed bone growth across the 16.5-cm³ defect of 1.82 ± 0.94 cm³. Histologic sections of the bridging tissues revealed callus originating from both the periosteal and endosteal surfaces, with fibrous tissue completing the bridging in all instances. Immunohistochemistry was used to evaluate the quality of the healing response. Clinical, radiographic, and histologic union was not achieved by 12 wk. This model may be effective for the investigation of surgical techniques and healing adjuncts for nonunion cases, where severe traumatic injury has led to significant bone loss.Abbreviations: BMP2, bone morphogenic protein 2; CATK, cathepsin K; VEGF, vascular endothelial growth factorThe human tibia is the most frequently broken long bone, often with significant bone loss.⁴ Segmental tibial defects can occur as a result of large tumor removal, trauma such as motor vehicle accidents, and more recently, blast injuries as seen with the escalating number of global conflicts. Treatment of these large bone and surrounding soft tissue defects is an ongoing, costly, and challenging clinical problem; no surgical technique has currently achieved preeminence.⁴ The general consensus on factors that affect healing include concomitant disease, age, and degree of trauma.⁵ When the first 2 factors, which are patient-related, are removed from the equation, healing is influenced by the size, anatomic location, and soft-tissue coverage of the defect. The ability to study these situations in a well-controlled, robust, and reproducible preclinical model would be advantageous to help establish effective surgical techniques and evaluate implants and materials.A literature review revealed that many ovine models for bone defects have been used, but all have limitations^{6,12,14,15,20,21,24,25,27,31,37,39,40} (Figure 1). Variations in protocols, such as age of the animals, size of the defect, and the bone and stabilization techniques used, limit meaningful comparison between studies.^33,34 Although some studies have investigated material performance in the healing of defects, they did not rigorously quantify control defects,^17,20 and others used no controls at all.³⁹ There is often no explanation regarding the use of a particular defect size, leading to the question of whether the defect size was critical.²⁴ The choice of bone used has been also varied; the femur,¹⁵ tibia,³⁷ and metatarsus⁴⁰ have all been studied. A noncritical-size defect implies that healing would eventually occur without the presence of any graft materials. One study,¹² for example, used a 3-cm defect at an average of 1.8 times the diameter of the tibias in question and found that empty controls achieved as much as 26% of the stiffness of an intact tibia after 12 wk. Stabilization methods include plating,^21,40 external fixtures,²⁰ intramedullary nails,^6,16 and a combination of intramedullary nails and plating.³⁷Open in a separate windowFigure 1.A limited summary of the many studies where a segmental tibial has been used with their references.The criteria used in the present study for a critical-size segmental tibial defect model were based on the following factors. The ovine tibia closely resembles that of the human tibia in terms of size, shape, and physical properties and is commonly used when studying human orthopedic diseases.^26,34 Intramedullary nailing has become the most commonly used method of tibial fracture fixation in human orthopedic surgery.^8,22 An 8-mm intramedullary nail is commonly used in the treatment of human fractures, further confirming the size similarity between the ovine and human tibiae.¹⁹The aim of this study was to establish and characterize a preclinical ovine 5-cm osteoperiosteal critical-size tibial segmental defect model in mature sheep. The endpoints included those commonly used clinically, such as radiography and microCT. Histology to investigate the degree of healing and immunohistochemistry to characterize the healing process were included to complete the evaluation process.