Conifer Woods of the Pliocene Age from Yunnan, China

The Tertiary floras play an integral role in understanding the biodiversity and interactions between climate and vegetation in Yunnan, China. The fossil spores, pollen grains, and leaves in this region have been investiaged intensively. In comparison, the woods have been studied relatively little. A large number of Pliocene wood specimens was collected from the opencast lignite coal mine of Hongxing situated in Changning County of Yunnan Province. Among the collection, Tsuga cf. dumosa (D. Don) Eichler and Pinus cf. armandii Franchet were identified based on wood structures. The subtle feature oftori extensions is reported in the wood of T. cf. dumosa. Considering the climatic requirements of modern T. dumosa and P.armandii, the two species of conifer described from Pliocene sediments probably grew in mountainous terrain at an elevation of approximately 2 300 m, in a cool and humid environment.     

The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965–1991: Part I: Prelude to Prions

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced by many scientists as `heretical'.This essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: (1) A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; (2) This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; (3) The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and (4) From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma, as outlined by both Francis Crick and James Watson, will be given. The developments in scrapie research from 1965 to 1972 will then be traced. This section will summarize many of the puzzling, non-viral-like properties of the scrapie agent. Alternative hypotheses to the viral explanation will also be presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid 1970s through 1991. The growing prominence of a protein-only model of infection will be balanced by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection.     

Lung Cancer: Are we up to the Challenge?

Lung cancer is the leading cause of cancer deaths worldwide among both men and women, with more than 1 million deaths annually. Non-small cell lung cancer (NSCLC) accounts for about 80% of all lung cancers.Although recent advances have been made in diagnosis and treatment strategies, the prognosis of NSCLC patients is poor and it is basically due to a lack of early diagnostic tools.However, in the last years genetic and biochemical studies have provided more information about the protein and gene's mutations involved in lung tumors. Additionally, recent proteomic and microRNA's approaches have been introduced to help biomarker discovery.Here we would like to discuss the most recent discoveries in lung cancer pathways, focusing on the genetic and epigenetic factors that play a crucial role in malignant cell proliferation, and how they could be helpful in diagnosis and targeted therapy.     

Assessing the contribution of products to the United Nations’ Sustainable Development Goals: a methodological proposal

Purpose

The 17 Sustainable Development Goals (SDGs) and their 169 targets pose the most important framework for sustainable development worldwide. However, the contributions of products and companies to the SDGs using social and environmental life cycle assessment (S-LCA; E-LCA) have not been thoroughly addressed in the scientific literature. The purpose of this research is therefore to identify product-related targets, derive suitable indicators and develop a social life cycle impact assessment (S-LCIA) method.

Methods

To systematically select product-related targets, two questions are developed. The questions ask whether a product (a) has a direct impact on the achievement of the target or (b) if the companies along the life cycle that produce or offer the product have a direct influence on the achievement of the respective target. Suitable indicators are derived and adapted from generally accepted frameworks such as the Global Indicator Framework (GIF-SDG). To develop an S-LCIA method, the targets are translated into conditions beneficial or damaging to the achievement of the target to estimate the socio-economic impact of the product using a scale from +1 to ?1. In cases where the targets remain vague, a systematic five-step approach to derive a quantifiable target involving five steps is applied.

Results and discussion

The main contribution of this paper is to propose a coherent method to measure the contribution of products to the targets. All 17 SDGs and 61 of the 169 targets (36%) were evaluated as product-related. For 57% of the product-related targets, indicators from the GIF-SDGs could at least partly be used after slight adaptations, while for the remaining 43% of the product-related targets, indicators were taken from other frameworks or sources or had to be added. In total, 45 indicators have been identified to be suitable for assessing the potential contribution of products to the 61 targets. To illustrate the systematic five-step approach to quantitatively assess the contribution of products to the targets, five types of contribution functions are presented in detail.

Conclusions

The presented method allows companies to analyse their impact and that of their products on the targets both within their own company and in the supply chain. As especially the latter is increasingly demanded by supply chain laws in different countries such as France, the Netherlands or the UK, the method fills an important research gap. However, future research to examine the proposed approach, the derived indicators and the impact assessment method is strongly encouraged.

     

The Prion Challenge to the `Central Dogma' of Molecular Biology, 1965–1991: Part II: The Problem with Prions

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced by many scientists as `heretical'.This two-part essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: (1) A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; (2) This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; (3) The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and (4) From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma was given, and the developments in scrapie research from 1965 to 1972 were traced. This section summarized many of the puzzling, non-virus-like properties of the scrapie agent. Alternative hypotheses to the viral explanation were presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid-1970s through 1991. The growing prominence of a protein-only model of infection will be countered by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection.     

Peliosanthes pachystachya，a new species of the Liliaceae from Yunnan，China

Peliosanthes pachystachya W.H.Chen&Y.M.Shui,a new species of Liliaceae from L chun County,SE Yunnan,is described and illustrated.The new species is similar to P.sinica Wang&Tang in the stolon with internodes ca.18cm long,but different by leaves9-13-nerved     

Differentiation of Nitrogen and Microbial Community in the Sediments from Lake Erhai,Yunnan–Kweichow Plateau,China

Abstract

As a famous plateau lake and a place rich in biodiversity located at the Hengduan Mountains, there is little research on microbial diversity and community composition in Erhai. In this study, 770,425 16S rRNA sequences had obtained at different depth samples. The abundance‐based coverage estimates (ACE), Chao1, and Shannon indices indicated the high abundance and diversity of Erhai sediment microorganisms. And they were obviously affected by human disturbance. Gammaproteobacteria, Deltaproteobacteria, Bacteroidia, Anaerolineae, Phycisphaerae, and Methanomicrobia were dominant bacteria and existed in almost all samples. The content of total nitrogen (TN) in sediments had a significant positive correlation between Syntrophus, Deltaproteobacteria, Desulfatiglans, Oxyphotobacteria, Clostridiales, Burkholderiaceae, Geobacter, Crenothrix species richness. Desulfobacca, Syntrophus, Deltaproteobacteria, Desulfatiglans, Gammaproteobacteria, Oxyphotobacteria, and Clostridiales were positively correlated with the nitrates in sediments. And the species richness of Desulfatiglans was correlated with NO₂ ^-. The RDA analysis was shown that dbRDA1 was affected mainly by the depth of lake, while the content of TN, NO₃ ^?, NO₂ ^?, and NH₄ ⁺ had the largest effect on dbRDA2. The results indicated the great relations between the diversity and composition of microbial communities and different forms of sediment nitrogen in Erhai lake sediments.     

Human health risk assessment of heavy metals in the soil–Panax notoginseng system in Yunnan province,China

In this study, a total of 69 topsoil samples and 10 Panax notoginseng samples from Yunnan Province were collected and the concentrations of As, Cd, Cu, Hg, Ni, Pb and Zn in all the samples were determined. The hazard index (HI), total carcinogenic risk (TCR) and estimated daily intake (EDI) of heavy metals were calculated to assess the health risk of P. notoginseng growers and consumers. The average concentrations of As, Cd, Cu, Hg, Ni, Pb and Zn in P. notoginseng planting soils are 43.6, 0.55, 50.8, 0.30, 73.4, 58.2, and 161 mg/kg, respectively. The average Nemerow integrated pollution index of heavy metals in soils is 1.8, indicating that the P. notoginseng planting soils are slightly polluted by those heavy metals. The average HI value is 1.29 and the TCR value of As is above the threshold value, suggesting that As pollution in soil has adverse impact on local growers' health. P. notoginseng is polluted by Cd, As and Pb. 39.1% of estimated daily intakes of As for P. notoginseng consumers through leaf consumption exceeding its permitted daily exposure dosages, suggesting that there is a potential health risk for P. notoginseng consumers to consume P. notoginseng leaves.     

Genetic Heterogeneity of the β-Globin Gene in Various Geographic Populations of Yunnan in Southwestern China

Objectives

The aim of this study was to investigate the geographic distribution of β-globin gene mutations in different ethnic groups in Yunnan province.

Methods

From 2004 to 2014, 1,441 subjects with hemoglobin disorders, identified by PCR-reverse dot blot and DNA sequencing, were studied according to ethnicity and geographic origin. Haplotypes were examined among 41 unrelated thalassemia chromosomes.

Results

Eighteen β-thalassemia mutations and seven hemoglobin variants were identified for 1,616 alleles in 22 different ethnic groups from all 16 prefecture-level divisions of Yunnan. The prevalence of β-thalassemia was heterogeneous and regionally specific. CD 41-42 (-TCTT) was the most prevalent mutation in the populations of northeastern Yunnan. CD 17 (A>T) was the most common mutation in the populations of southeastern Yunnan, especially for the Zhuang minority, whereas Hb E (CD 26, G>A) was the most prevalent mutation in populations of southwestern Yunnan, especially for the Dai minority. Among the seven types of haplotypes identified, CD 17 (A>T) was mainly linked to haplotype VII (+ - - - - - +) and IVS-II-654 (C>T) was only linked to haplotype I (+ - - - - + +).

Conclusion

Our data underline the heterogeneity of β-globin gene mutations in Yunnan. This distribution of β-globin mutations in the geographic regions and ethnic populations provided a detailed ethnic basis and evolutionary view of humans in southern China, which will be beneficial for genetic counseling and prevention strategies.     

Late Darriwilian–early Katian (Ordovician) ostracods of northeastern Yunnan,Southwest China

Ordovician silicified ostracods of the western Yangtze Platform, South China, are documented for the first time from the Huadan Formation of Qiaojia County, northeastern Yunnan Province, Southwest China. Twenty-one species of 17 genera are identified with new taxa including Vendona spinifera n. sp. and Nikitinella songliangensis n. sp. These two species, together with Medianella gigantea are the most common constituents of the fauna. Faunal comparison shows close connections between South China, Baltica, the Argentine Precordillera, Kazakhstan, Tarim, and Sibumasu during this time interval. This fauna is considered to be related to a nearshore carbonate environment, and biostratigraphical analysis of it supports a late Darriwilian to early Katian age for the Huadan Formation.     

Modulation of the albumin–paraoxon interaction sites by fatty acids: Analysis by the molecular modeling methods

It is known that albumin can break the ester bonds in organophosphorus compounds (OPs). Amino acids responsible for esterase and pseudoesterase activity of albumin towards OPs are still not determined. It is assumed that Sudlow’s site I with residue Tyr150 exhibits the “true” esterase activity; and Sudlow’s site II containing residue Tyr411, a pseudoesterase one. Binding of fatty acids to albumin affects the efficiency of its interaction with xenobiotics; however, the effect of fatty acids on the interaction of albumin with OPs was not studied. The purpose of this work was to study the interaction of OPs with potential sites of albumin enzymatic activity and to examine the effect of fatty acids on the efficiency of such interaction using the molecular modeling methods by the example of paraoxon, a known inhibitor of acetylcholinesterase, and oleic acid. The structures of the protein complexes with paraoxon and oleic acid were determined by the molecular docking procedure; the conformational changes were calculated by the molecular dynamics method. It has been shown that sorption of oleic acid in one of the fatty acid-binding sites leads to the conformational changes in Sudlow’s sites I and II due to a “reversal” of the side chains of Arg410 and Arg257 residues by 90°. It has been found that this change in geometry reduces the affinity of Sudlow’s site I and increases the Sudlow’s site II affinity to paraoxon. The amino acid residue Ser193, which was previously identified as a site of possible albumin esterase activity, is not able to bind paraoxon efficiently. It is assumed that its activity can be affected by the interaction of the oleic acid molecules with other fatty acid-binding sites. It is hypothesized that the lesser toxicity of paraoxon compared to soman may be associated not only with its lower inhibitory activity against cholinesterases, but also with the increased affinity of paraoxon to albumin. It was concluded that albumin may serve as an alternative means of OP detoxification.     

Quantitative analysis of five sterols in amniotic fluid by GC–MS: Application to the diagnosis of cholesterol biosynthesis defects

Cholesterol and its precursors, namely 7-dehydrocholesterol, desmosterol and lathosterol are important biochemical markers of cholesterol biosynthesis, and their quantification in body fluids is useful for the diagnosis of cholesterol biosynthesis pathway disorders. A rapid and sensitive gas chromatographic–mass spectrometric method was developed and validated for quantitative analysis of five sterols (cholesterol, 7-dehydrocholesterol, desmosterol, lathosterol and sitosterol) in amniotic fluid. The method was linear for all compounds (r² > 0.99), and intra and inter-assay coefficients of variation were typically below 5%, and inaccuracy was within a ±12% interval. The method was applied to 330 amniotic fluid samples, grouped by gestational age between 13 and 22 weeks of pregnancy, in order to establish reference intervals for sterols in this specimen. The obtained concentrations (μmol/L) for each sterol was as follows: 22.1758 ± 4.2716 at 13 weeks and 78.5082 ± 12.9041 at 22 weeks for cholesterol; 0.0039 ± 0.0007 at 13 weeks and 0.1150 ± 0.0212 at 22 weeks for 7-dehydrocholesterol; 0.1562 ± 0.0406 at 13 weeks and 0.7691 ± 0.0821 at 22 weeks for desmosterol; 0.0272 ± 0.0035 at 13 weeks and 0.8551 ± 0.1791 at 22 weeks for lathosterol; and 0.0404 ± 0.0039 at 13 weeks and 0.2326 ± 0.0386 at 22 weeks for sitosterol. The method was also applied to one pathological sample that showed decreased levels of cholesterol, and higher concentration of 7-dehydrocholesterol, which is consistent with a 7-dehydrocholesterol-reductase deficiency. Our results showed that as long as pregnancy goes on, the concentrations of cholesterol and precursors increase in amniotic fluid, which is related to the increased need for cholesterol by the fetus. The reference range of each sterol in amniotic fluid was calculated at different gestational ages and will be useful for the interpretation and validation of biochemical prenatal diagnosis of inborn errors of sterol biosynthesis.     

Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province,China During 2009–2016

Previous studies indicated that fruit bats carry two betacoronaviruses,BatCoV HKU9 and BatCoV GCCDC1.To investigate the epidemiology and genetic diversity of these coronaviruses,we conducted a longitudinal surveillance in fruit bats in Yunnan province,China during 2009–2016.A total of 59(10.63%)bat samples were positive for the two betacorona-viruses,46(8.29%)for HKU9 and 13(2.34%)for GCCDC1,or closely related viruses.We identified a novel HKU9 strain,tentatively designated as BatCoV HKU9-2202,by sequencing the full-length genome.The BatCoV HKU9-2202 shared 83%nucleotide identity with other BatCoV HKU9 stains based on whole genome sequences.The most divergent region is in the spike protein,which only shares 68%amino acid identity with BatCoV HKU9.Quantitative PCR revealed that the intestine was the primary infection organ of BatCoV HKU9 and GCCDC1,but some HKU9 was also detected in the heart,kidney,and lung tissues of bats.This study highlights the importance of virus surveillance in natural reservoirs and emphasizes the need for preparedness against the potential spill-over of these viruses to local residents living near bat caves.     

Differential regulation of the calpain–calpastatin complex by the L-domain of calpastatin

Here we demonstrate that the presence of the L-domain in calpastatins induces biphasic interaction with calpain. Competition experiments revealed that the L-domain is involved in positioning the first inhibitory unit in close and correct proximity to the calpain active site cleft, both in the closed and in the open conformation. At high concentrations of calpastatin, the multiple EF-hand structures in domains IV and VI of calpain can bind calpastatin, maintaining the active site accessible to substrate. Based on these observations, we hypothesize that two distinct calpain–calpastatin complexes may occur in which calpain can be either fully inhibited (I) or fully active (II). In complex II the accessible calpain active site can be occupied by an additional calpastatin molecule, now a cleavable substrate. The consequent proteolysis promotes the accumulation of calpastatin free inhibitory units which are able of improving the capacity of the cell to inhibit calpain. This process operates under conditions of prolonged [Ca^2 +] alteration, as seen for instance in Familial Amyotrophic Lateral Sclerosis (FALS) in which calpastatin levels are increased. Our findings show that the L-domain of calpastatin plays a crucial role in determining the formation of complexes with calpain in which calpain can be either inhibited or still active. Moreover, the presence of multiple inhibitory domains in native full-length calpastatin molecules provides a reservoir of potential inhibitory units to be used to counteract aberrant calpain activity.     

Response to Dangl: Complex harmonies of the host–pathogen interaction

In the accompanying Research Focus article that summarises our recent research article [1], Jeffery Dangl likens the interplay of the intracellular pathogen Salmonella enterica serovar Typhimurium with the host resistance protein Nramp1 to the response of a congregation to the teachings of a preacher. In principle, this is a fair interpretation of what we believe to be occurring on the molecular level between host and pathogen within the limited scope of our experiments. However, as with most biological systems, we believe that this analogy might be too simplistic. As Dangl points out, Nramp1 ‘might have a multitude of messages that it sends to different vacuolar inhabitants’. This cannot exclude the fact that the effects of Nramp1 on any single pathogen are pleiotropic and that we focused solely on one aspect of Nramp1 function in our studies, that is, divalent cation limitation. Therefore, we suggest that the interplay between innate host defences and pathogens is far more complex than simple call-and-response. Instead, we propose that it is more like a musical round, where one instrument makes the initial statement of the tune followed by the response of a second instrument, building over successive entrances to a complex orchestral whole. As a case in point, we wish to draw the reader's attention to the complex influences of both Nramp1 and S. enterica Typhimurium on the generation of toxic oxygen and nitrogen intermediates by the host during infection.     

Analysis by DC–EPG of the resistance to Bemisia tabaci on an Mi-tomato line

The tomato Mi gene confers resistance to nematodes, Meloidogyne spp., and to the potato aphid, Macrosiphum euphorbiae (Thomas). Previous greenhouse choice assays with Bemisia tabaci (Gennadius) showed that tomato commercial varieties carrying this gene had significantly lower values of host suitability and whitefly reproduction than varieties lacking Mi. This indicated that Mi, or another gene in its region, could regulate partial resistance. In order to characterise this resistance, probing and feeding behaviour of Bemisia tabaci B-biotype was studied with DC Electrical Penetration Graph (EPG) technique on the near-isogenic tomato lines Moneymaker (without Mi) and Motelle (carrying Mi). Significant differences (P < 0.05) between tomato lines were found in EPG parameters related to epidermis and/or mesophyll tissues. On Motelle, a lower percentage of whiteflies achieved phloem phase and they made more probes before attaining first phloem phase, had a higher ratio (number of probes before first phloem phase)/(total number of probes), had a longer total duration of non-probing time, and a longer time before making the first intracellular puncture and before making the first phloem phase. In contrast, most of the parameters related to phloem phase were found not to differ significantly between these near-isogenic lines. The behavioural data strongly suggest that the partial resistance in the variety Motelle is due to factors in the epidermis and/or mesophyll that inhibit the whiteflies from reaching phloem sieve elements. However, once the stylets reach a sieve element, whitefly behaviour did not differ between the two varieties. Thus, phloem sap of the two varieties appears to be equally acceptable to the whiteflies. Further studies are necessary to provide a better understanding of these mechanisms of resistance to whiteflies in tomatoes.     

Quantitative affinity electrophoresis of RNA–small molecule interactions by cross-linking the ligand to acrylamide

We show that the affinity electrophoresis analysis of RNA–small molecule interactions can be made quantifiable by cross-linking the ligand to the gel matrix. Using an RNA–aminoglycoside model system to verify our method, we attached an acryloyl chloride molecule to the aminoglycosides paromomycin and neomycin B to synthesize an acrylamide–aminoglycoside monomer. This molecule was then used as a component in gel polymerization for affinity electrophoresis, covalently attaching an aminoglycoside molecule to the gel matrix. To test RNA binding to the cross-linked aminoglycosides, we used the aminoglycoside binding RNA molecule derived from thymidylate synthase messenger RNA (mRNA) that contains a C–C mismatch. Binding is indicated by the difference in RNA mobility between gels with cross-linked ligand, with ligand embedded during polymerization, and with no ligand present. Critically, the predicted straight line relationship between the reciprocal of the relative migration of the RNA and the ligand concentration is obtained when using cross-linked aminoglycosides, whereas a straight line is not obtained using embedded aminoglycosides. Average apparent dissociation constants are determined from the slope of the line from these plots. This method allows an easy quantitative comparison between different nucleic acid molecules for a small molecule ligand.     

Trapping of γ-Decalactone by Adsorption on Hydrophobic Sorbents : Application to the bioconversion of methyl ricinoleate by the yeast Sporidiobolus salmonicolor

Trapping by adsorption on hydrophobic porous polymers was used to selectively remove -decalactone from the complex bioconversion medium. Several sorbents were tested : activated carbon, and three porous polystyrene-type polymers (Porapak Q, Chromosorb 105, and Resin SM4). The sorption isotherms were determined in water and in a model bioconversion medium without microorganisms. In the last part of the study, the application to the production of -decalactone by Sporidiobolus salmonicolor was carried out. Hydrophobic porous adsorbents are compatible with the bioconversion and protect the yeast from the toxic effect of -decalactone.