Energy balances and greenhouse gas emissions of palm oil biodiesel in Indonesia

This study presents a cradle‐to‐gate assessment of the energy balances and greenhouse gas (GHG) emissions of Indonesian palm oil biodiesel production, including the stages of land‐use change (LUC), agricultural phase, transportation, milling, biodiesel processing, and comparing the results from different farming systems, including company plantations and smallholder plantations (either out growers or independent growers) in different locations in Kalimantan and Sumatra of Indonesia. The findings demonstrate that there are considerable differences between the farming systems and the locations in net energy yields (43.6–49.2 GJ t^?1 biodiesel yr^?1) as well as GHG emissions (1969.6–5626.4 kg CO_2eq t^?1 biodiesel yr^?1). The output to input ratios are positive in all cases. The largest GHG emissions result from LUC effects, followed by the transesterification, fertilizer production, agricultural production processes, milling, and transportation. Ecosystem carbon payback times range from 11 to 42 years.     

Effect of accelerated electron beam on mechanical properties of human cortical bone: influence of different processing methods

Accelerated electron beam (EB) irradiation has been a sufficient method used for sterilisation of human tissue grafts for many years in a number of tissue banks. Accelerated EB, in contrast to more often used gamma photons, is a form of ionizing radiation that is characterized by lower penetration, however it is more effective in producing ionisation and to reach the same level of sterility, the exposition time of irradiated product is shorter. There are several factors, including dose and temperature of irradiation, processing conditions, as well as source of irradiation that may influence mechanical properties of a bone graft. The purpose of this study was to evaluate the effect e-beam irradiation with doses of 25 or 35?kGy, performed on dry ice or at ambient temperature, on mechanical properties of non-defatted or defatted compact bone grafts. Left and right femurs from six male cadaveric donors, aged from 46 to 54?years, were transversely cut into slices of 10?mm height, parallel to the longitudinal axis of the bone. Compact bone rings were assigned to the eight experimental groups according to the different processing method (defatted or non-defatted), as well as e-beam irradiation dose (25 or 35?kGy) and temperature conditions of irradiation (ambient temperature or dry ice). Axial compression testing was performed with a material testing machine. Results obtained for elastic and plastic regions of stress-strain curves examined by univariate analysis are described. Based on multivariate analysis, including all groups, it was found that temperature of e-beam irradiation and defatting had no consistent significant effect on evaluated mechanical parameters of compact bone rings. In contrast, irradiation with both doses significantly decreased the ultimate strain and its derivative toughness, while not affecting the ultimate stress (bone strength). As no deterioration of mechanical properties was observed in the elastic region, the reduction of the energy absorption capacity of irradiated bone rings apparently resulted from changes generated by irradiation within the plastic strain region.     

Effect of gamma irradiation on mechanical properties of human cortical bone: influence of different processing methods

The secondary sterilisation by irradiation reduces the risk of infectious disease transmission with tissue allografts. Achieving sterility of bone tissue grafts compromises its biomechanical properties. There are several factors, including dose and temperature of irradiation, as well as processing conditions, that may influence mechanical properties of a bone graft. The purpose of this study was to evaluate the effect of gamma irradiation with doses of 25 or 35?kGy, performed on dry ice or at ambient temperature, on mechanical properties of non-defatted or defatted compact bone grafts. Left and right femurs from six male cadaveric donors aged from 46 to 54?years, were transversely cut into slices of 10?mm height, parallel to the longitudinal axis of the bone. Compact bone rings were assigned to the eight experimental groups according to the different processing method (defatted or non-defatted), as well as gamma irradiation dose (25 or 35?kGy) and temperature conditions of irradiation (ambient temperature or dry ice). Axial compression testing was performed with a material testing machine. Results obtained for elastic and plastic regions of stress-strain curves examined by univariate analysis are described. Based on multivariate analysis it was found that defatting of bone rings had no significant effect on any mechanical parameter studied, whereas irradiation with both doses decreased significantly the ultimate strain and its derivative toughness. The elastic limit and resilience were significantly increased by irradiation with the dose 25?kGy, but not 35?kGy, when the time of irradiation was longer. Additionally, irradiation at ambient temperature decreased maximum load, elastic limit, resilience, and ultimate stress. As strain in the elastic region was not affected, decreased elastic limit resulted in lower resilience. The opposite phenomenon was observed in the plastic region, where in spite of the lower ultimate stress, the toughness was increased due to the increase in the ultimate strain. The results of our study suggest that there may be an association between mechanical properties of bone tissue grafts and the damage process of collagen structure during gamma irradiation. This collagen damage in cortical bone allografts containing water does not depends on the temperature of irradiation or defatting during processing if dose of gamma irradiation does not exceed 35?kGy.     

The effect of embryonic development on metal and calcium content in eggs and eggshells in a small passerine

Published information relating to changes in the chemical element content of avian eggs caused by embryonic development is extremely scarce, although it may be crucial for understanding both the presence of anthropogenic pollutants as well as physiological levels of micronutrients. We assessed the variation in concentrations of calcium (Ca) and magnesium (Mg) and nine trace elements: seven essential (chromium (Cr), copper (Cu), nickel (Ni), manganese (Mn), iron (Fe), cobalt (Co) and zinc (Zn)) and two non‐essential (lead (Pb) and cadmium (Cd)) in shells and contents (both egg yolk and egg white) of embryonated and non‐embryonated eggs. We investigated the eggs of the Eurasian Reed Warbler Acrocephalus scirpaceus, a large proportion of whose eggs are infertile in our study population (almost 43% of clutches contain unhatched eggs) as well as significant embryo‐induced eggshell thinning at the equator of embryonated eggs. We found significantly higher concentrations (≥ 22.7%) of all the focal elements in the contents of embryonated eggs in comparison with non‐embryonated eggs, and a very pronounced one for Ca (nearly twice as high). The shells of embryonated eggs contained significantly higher concentrations of Zn (104.1%), Fe (56.5%), Pb (32.8%) and Cu (28.0%) but significantly lower ones of Co (8.9%) and Ca (9.3%) than the shells of non‐embryonated eggs. The simultaneous higher concentrations of all elements in the content of thinner‐shelled embryonated eggs suggest the parallel transfer of these elements along with Ca resorption from the shell into the egg interior during embryo formation. The higher concentration of most elements in the thinner shells of embryonated eggs may be indicative of the maternal deposition of some of these elements in a shell layer not subject to embryonic depletion, or in the eggshell membrane. Our results highlight the need for the careful selection of egg samples, which should differentiate between embryonated and non‐embryonated eggs in the analytical treatment of eggs and eggshells.     

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: a case study using molecular approaches

In Middle European suburban environments green algae often cover open surfaces of artificial hard substrates. Microscopy reveals the Apatococcus/Desmococcus morphotype predominant over smaller coccoid forms. Adverse conditions such as limited water availability connected with high PAR and UV irradiance may narrow the algal diversity to a few specialists in these subaerial habitats. We used rRNA gene cloning/sequencing from both DNA extracts of the biofilms without culturing as well as cultures, for the unambiguous determination of the algal composition and to assess the algal diversity more comprehensively. The culture independent approach revealed mainly just two genera (Apatococcus, Trebouxia) for all study sites and five molecular operational taxonomic units (OTUs) for a particular study site, which based on microscopic observation was the one with the highest morphological diversity. The culture approach, however, revealed seven additional OTUs from five genera (Chloroidium, Coccomyxa, Coenochloris, Pabia, Klebsormidium) and an unidentified trebouxiophyte lineage for that same site; only two OTUs were shared by both approaches. Two OTUs or species were recovered for which references have been isolated only from Antarctica so far. However, the internal transcribed spacer (ITS) sequence differences among them supported they are representing distinct populations of the same species. Within Apatococcus five clearly distinct groups of ITS sequences, each putatively representing a distinct species, were recovered with three or four such ITS types co‐occurring at the same study site. Except for the streptophyte Klebsormidium only members of Trebouxiophyceae were detected suggesting these algae may be particularly well‐adapted to subaerial habitats.     

A Highlights from MBoC Selection: Ccdc11 is a novel centriolar satellite protein essential for ciliogenesis and establishment of left–right asymmetry

The establishment of left–right (L-R) asymmetry in vertebrates is dependent on the sensory and motile functions of cilia during embryogenesis. Mutations in CCDC11 disrupt L-R asymmetry and cause congenital heart disease in humans, yet the molecular and cellular functions of the protein remain unknown. Here we demonstrate that Ccdc11 is a novel component of centriolar satellites—cytoplasmic granules that serve as recruitment sites for proteins destined for the centrosome and cilium. Ccdc11 interacts with core components of satellites, and its loss disrupts the subcellular organization of satellite proteins and perturbs primary cilium assembly. Ccdc11 colocalizes with satellite proteins in human multiciliated tracheal epithelia, and its loss inhibits motile ciliogenesis. Similarly, depletion of CCDC11 in Xenopus embryos causes defective assembly and motility of cilia in multiciliated epidermal cells. To determine the role of CCDC11 during vertebrate development, we generated mutant alleles in zebrafish. Loss of CCDC11 leads to defective ciliogenesis in the pronephros and within the Kupffer’s vesicle and results in aberrant L-R axis determination. Our results highlight a critical role for Ccdc11 in the assembly and function of motile cilia and implicate centriolar satellite–associated proteins as a new class of proteins in the pathology of L-R patterning and congenital heart disease.     

Protein purification and crystallization artifacts: The tale usually not told

The misidentification of a protein sample, or contamination of a sample with the wrong protein, may be a potential reason for the non‐reproducibility of experiments. This problem may occur in the process of heterologous overexpression and purification of recombinant proteins, as well as purification of proteins from natural sources. If the contaminated or misidentified sample is used for crystallization, in many cases the problem may not be detected until structures are determined. In the case of functional studies, the problem may not be detected for years. Here several procedures that can be successfully used for the identification of crystallized protein contaminants, including: (i) a lattice parameter search against known structures, (ii) sequence or fold identification from partially built models, and (iii) molecular replacement with common contaminants as search templates have been presented. A list of common contaminant structures to be used as alternative search models was provided. These methods were used to identify four cases of purification and crystallization artifacts. This report provides troubleshooting pointers for researchers facing difficulties in phasing or model building.     

m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants

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