RivFishTIME: A global database of fish time-series as a currency for global change ecology research in riverine systems

Motivation We compiled a global database of long-term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones. Main types of variables contained The database includes 11,386 time-series of riverine fish community catch data, including 646,270 species-specific abundance records, together with metadata related to the geographical location and sampling methodology of each time-series. Spatial location and grain The database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins world-wide. Time period and grain The database encompasses the period 1951–2019. Each time-series is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years). Major taxa and level of measurement The database includes 944 species of ray-finned fishes (Class Actinopterygii). Software format csv. Main conclusion Our collective effort provides the most comprehensive long-term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm

Improved nucleic acid testing strategies to detect and discriminate veterinary relevant Mycobacterium tuberculosis complex members

Os membros do complexo Mycobacterium tuberculosis (MTC) são agentes causadores de tuberculose em humanos e animais. A tuberculose bovina tem sido sujeita nas últimas décadas a programas de erradicação bastante dispendiosos, na maioria dos países desenvolvidos, envolvendo a análise laboratorial de tecidos de animais suspeitos para a detecção dos membros do MTC, nomeadamente Mycobacterium bovis. O diagnóstico definitivo é obtido através da cultura bacteriológica, o que pode levar 6-12 semanas, período durante o qual a carcaça do animal suspeito e a exploração de origem permanecem sob embargo sanitário. Neste trabalho, descreve-se um protocolo de extracção de DNA de fácil utilização adaptado aos tecidos, o qual é acoplado a um semi-nested PCR em tempo real, utilizando como alvo a IS6110, por forma a melhorar a detecção directa de bactérias pertencentes ao MTC em animais, abreviando o período necessário ao diagnóstico. O ensaio foi avaliado num grupo de 128 amostras de tecido provenientes de bovinos, javalis, veados e raposas. O desempenho global do teste corresponde a uma sensibilidade e especificidade de diagnóstico de 98,2% e 88,7%, respectivamente. Foi observado um coeficiente kappa de 0,859 entre o ensaio de semi-nested PCR e a cultura bacteriológica. Este ensaio permite a detecção rápida de micobactérias tuberculosas em amostras de animais com alta sensibilidade e especificidade, sendo acessível e de baixo custo para uma utilização num laboratório de diagnóstico veterinário. As espécies do MTC são geneticamente muito semelhantes, mas podem divergir na sua epidemiologia, nomeadamente na distribuição geográfica e preferência pelo hospedeiro, factores de virulência e padrões de susceptibilidade antimicrobiana. No entanto, o diagnóstico laboratorial convencional não diferencia rotineiramente as espécies do MTC. Foi desenvolvido um algoritmo de identificação rápido e robusto, baseado em PCR em tempo real, dirigido para cinco alvos genómicos para a identificação das espécies do MTC vulgarmente associadas à tuberculose nos bovinos e outros animais. O primeiro passo permite a confirmação dos membros do MTC nas culturas, através da detecção da IS6110, ou como uma espécie micobacteriana, pela presença do 16S rDNA. Se uma espécie do MTC for identificada, o segundo passo do algoritmo permite avaliar a presença ou ausência das regiões genómicas RD1, RD4 e RD9. O padrão correspondente permite inferir a espécie do isolado como M. tuberculosis (se todas as RDs estiverem presentes), M. caprae (se apenas a RD1 e RD4 estiverem presentes) ou M. bovis (se apenas a RD1 estiver presente). O algoritmo de identificação desenvolvido demonstrou um coeficiente kappa de 0,970 com o resultado da análise bacteriológica. O ensaio pode ser implementado em laboratórios de diagnóstico veterinário, especialmente em laboratórios de referência. Tem-se registado uma procura crescente por métodos de diagnóstico de doenças infecciosas rápidos, de fácil utilização e acessíveis, passíveis de serem utilizados em pontos-de-decisão. A detecção dos membros do MTC é geralmente realizada por diversos métodos convencionais baseados na cultura, que normalmente necessitam de oito semanas. Foram também desenvolvidas estratégias de diagnóstico molecular, mas a maioria requer operadores qualificados e equipamentos e infra-estruturas sofisticadas. Recentemente, a técnica de Loop-Mediated Isothermal Amplification (LAMP) mostrou-se promissora para o desenvolvimento de testes rápidos, de baixo custo, sensíveis e específicos para a detecção de agentes patogénicos. Neste trabalho, foram optimizados dois sistemas LAMP em formato duplex (dLAMP) para a identificação do MTC e Mycobacterium tuberculosis, e do MTC e M. bovis, apresentando valores de sensibilidade e especificidade comparáveis a outras abordagens em que se utiliza o PCR convencional. Os resultados das amplificações são avaliados colorimetricamente utilizando dispositivos de fluxo lateral, simples e comercialmente disponíveis, para a detecção de ácidos nucleicos (NALF). Os resultados apresentados nesta dissertação contribuem para a melhoria das estratégias de diagnóstico molecular existentes no combate à tuberculose animal.Members ofMycobacterium tuberculosiscomplex (MTC)are causative agents of tuberculosis in both humans and animals.Bovine tuberculosis has been tackled for decades by costly eradication programs in most developed countries, involving thelaboratorial testing of tissue samples from allegedly infected animals for detection of MTCmembers, namely Mycobacterium bovis. Definitive diagnosis is usually achieved by bacteriological culture, which may take up to 6-12 weeks, during which the suspectanimal carcass and herd are under sanitary arrest.In this work we describea user-friendly DNA extraction protocol adapted for tissues andcoupled with an IS6110-targeted semi-nested real-time PCR assay to enhance the direct detection of MTC bacteria in animal specimens, reducing the time to achieve a diagnosis. The assay was evaluated with a group of 128 freshtissue specimens collected from bovines, wild boars, deer and foxes. Overall, the full test performance corresponds to a diagnostic sensitivity and specificity of 98.2% and 88.7%, respectively. An observed kappa coefficient was estimated in 0.859 for the overall agreement between the semi-nested PCR assay and the bacteriological culture. This novel IS6110-targeted assay allows the fast detection of tuberculous mycobacteria in animal specimens with very high sensitivity and specificity, beingamenable and cost effective for use in the routine veterinary diagnostic laboratory with further automation possibilities.MTC species are genetically very similar but may differ in their epidemiology, namely geographic distributionand host preferences, virulence traits and antimicrobial susceptibility patterns. However, the conventional laboratory diagnosis does not routinely differentiate between the species ofthe MTC. We developedarapid and robust two-step five-target probe-based real-time PCR identification algorithm, based on genomic deletion analysis, to identify the MTC species most commonly associated with TB in livestock and other animals.The first step allows the confirmation of the cultures as MTC members, by targeting their IS6110element, or as a mycobacterial species, if only a 16S rDNA product is detected in the duplex amplification reaction. If a MTC member is identified, the second amplification step allows to assess the presence or absence of the RD1, RD4 and RD9 genomic regions. The correspondent pattern allows to infer the species of the isolate as M. tuberculosis(if all RDs are present), M. caprae(if only RD1 and RD4 are present) and M. bovis(if only RD1 is present). The identification algorithmdevelopedpresented an almost perfect agreement with the results of the routine bacteriological analysis, with a kappa coefficient of 0.970.The assay is able to be adaptable to automation and implementation in the routine diagnostics framework of veterinary diagnostics laboratories, with a particular focus for reference laboratories. Rapid, user-friendly and affordable diagnostictests for use in the point-of-decision or point-of-care settings are in high demand globally. Detection of MTC members is generally performedby cumbersome conventional culture-based methods,whichusually takesup to eight weeks.Molecular diagnosis strategies were also developed but most of these requires skilled operators and sophisticatedequipmentsand facilities. More recently, the Loop-Mediated Isothermal Amplification (LAMP) technique showed promise for the development of rapid, low-cost, sensitive and specific testsfor detecting pathogens.In this work we have optimized duplex LAMP (dLAMP) assays for the identification of MTC and Mycobacterium tuberculosis, and MTCand M. bovis, presenting similar sensitivities and specificitieswhen compared to standard PCRapproaches. The amplification results are assessed colorimetricallyby using simple and commercially available nucleic acid lateral flow (NALF) strips.With the work described in this dissertation we aim to modestly contributeto the improvement of the existing molecular diagnosis strategiesto combat animal tuberculosis

Laser-induced generation of singlet oxygen and its role in the cerebrovascular physiology

For over 55 years, laser technology has expanded from laboratory research to widespread fields, for example telecommunication and data storage amongst others. Recently application of lasers in biology and medicine presents itself as one of the emerging areas. In this review, we will outline the recent advances in using lasers for the generation of singlet oxygen, traditionally used to kill tumour cells or induce thrombotic stroke model due to damage vascular effects. Over the last two decade, completely new results on cerebrovascular effects of singlet oxygen generated during photodynamic therapy (PDT) have been shown alongside promising applications for delivery of drugs and nanoparticles into the brain for therapy of brain cancer. Furthermore, a "gold key” has been found to overcome the limitations of PDT, such as low light penetration and high toxicity of photosensitizers, by direct generation of singlet oxygen using quantum-dot laser diodes emitting in the near infrared (NIR) spectral range. It is our motivation to highlight these pioneering results in this review, to improve understanding of the biological role of singlet oxygen and to provide new perspectives for improving clinical application of laser based therapy in further research

Optimization of HPLC Detection of PMP Derivatives of Carbohydrates

Detection of carbohydrates has always been a big challenge in the world, which is still attracting numerous researchers to develop different methods to overcome various difficulties. Reducing sugars, a special group of carbohydrates containing a reducing end, have provided a possibility to combine one or more chromophores to facilitate the carbohydrate detection in spite of the lack of chromophoric group in original carbohydrates. After such kind of chemical derivatizations, the sugar derivatives can be analyzed by high performance liquid chromatography (HPLC) with ultraviolet detector (UV) and diode array detector (DAD), which have been the most common methods for the carbohydrate detection. In order to optimize the sugar detection via the HPLC-UV and/or DAD, this study applied the chemical derivatization to add an extra luminophore into carbohydrates molecules, for which 1-phenyl-3-methyl-5-pyrazolone (PMP) was used in this experiment. The optimal conditions for derivatizations of glucose and glucosamine with PMP were obtained through the response surface methodology (RSM) experimental design, which suggested the optimal conditions, under a fixed value at pH 13 of the buffer solution, for the glucose-PMP and glucosamine-PMP derivatizations at 71°C for 134 minutes and 73°C for 96 minutes, respectively. The delicate difference among the optimal conditions might result from the difference of the inner-structure and inner environmental pH values of the carbohydrates. Nevertheless, this method has been proven to be a feasible and practical method with high sensitivity to determine the most monosaccharides except fructose, and disaccharides such as lactose and maltose, as well as oligosaccharides which contain the reducing end. In addition to the effect of inner pH environment, multiple sugar rings and optical isomerism of carbohydrates might also play important roles in the yield of sugar-PMP derivatives. Furthermore, this research involved the study of the detective power in terms of the detective sensitivity, accuracy and linearity of two common detectors, i.e., DAD and evaporative light scattering detector (ELSD), on the sugar-PMP derivatives, and the efficiency in terms of the separation capability of two common HPLC columns, i.e., C18 column and amide column. Because of different principles of DAD and ELSD in chemical detection, both popular detectors have different sensitivities and selectivities for carbohydrates. DAD is able to analyze the sugar-PMP derivatives, while ELSD is good at detecting both the PMP free sugars, sugar PMP derivatives and other sugar derivatives such as sugar alcohols, etc. Moreover, the results have demonstrated that the amide column could efficiently separate the PMP free carbohydrates rather than the sugar-PMP derivatives, and on the contrary, the C18 column was able to separate the sugar-PMP derivatives rather than the sugar themselves

New Mexico Daily Lobo, Volume 079, No 123, 4/2/1976

New Mexico Daily Lobo, Volume 079, No 123, 4/2/1976https://digitalrepository.unm.edu/daily_lobo_1976/1050/thumbnail.jp

Green phosphorescent Zn(II) halide complexes with N,N,N′,N′‐tetramethyl‐P‐indol‐1‐ylphosphonic diamide as ligand

Tetrahedral Zn(II) complexes having general formula [ZnX2{O=P(NMe2)2Ind}2] (X= Cl, Br, I, NCS) were isolated from the reaction between the indol-1-yl substituted phosphoramide N,N,N',N'-tetramethyl-P-indol-1-ylphosphonic diamide (O=P(NMe2)2Ind) and anhydrous Zn(II) precursors under mild conditions. The structures of the three halide derivatives were ascertained by single-crystal X-ray diffraction. The bromo- and iodo-derivatives revealed to be appreciably luminescent in the green region upon excitation with light below 300 nm, with emission bands centred between 520 and 530 nm. The large Stokes shifts and the excited state lifetimes in the milliseconds range indicate that triplet excited states are involved in the emission. TD-DFT calculations indicated that the transition responsible of the luminescence is ligand-centred (3LC)

Rotational control of reactivity: Reaction of SiO+^+ ions in extreme rotational states

Optical pumping of molecules provides unique opportunities for the control of chemical reactions at a wide range of rotational energies. Chemical reactivity for the hydrogen abstraction reaction SiO$^+$ + H$_2$ $\rightarrow$ SiOH$^+$ + H is investigated in an ion trap. The SiO$^+$ cation is prepared with a narrow rotational state distribution, including super-rotor states with rotational quantum number $\it{(j)}$ as high as 170 using a broad-band optical pumping method. The super-rotor states of SiO$^+$ are shown to substantially enhance the reaction rate, a trend reproduced by complementary theoretical studies. The mechanism for the rotational enhancement of the reactivity is revealed to be a strong coupling of the SiO$^+$ rotational mode with the reaction coordinate at the transition state on the dominant dynamical pathway. This work reports for the first time a chemical reaction with extreme rotational excitation of a reactant and its kinetic characterization

Force transduction and lipid binding in MscL: a continuum-molecular approach

The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this detailed chemical information and current mechanical models of MscL gating. Here, we investigate the MscL bilayer-protein interface through molecular dynamics simulations, and take a combined continuum-molecular approach to connect chemistry and mechanics. We quantify the effect of membrane tension on the forces acting on the surface of the channel, and identify interactions that may be critical in the force transduction between the membrane and MscL. We find that the local stress distribution on the protein surface is largely asymmetric, particularly under tension, with the cytoplasmic side showing significantly larger and more localized forces, which pull the protein radially outward. The molecular interactions that mediate this behavior arise from hydrogen bonds between the electronegative oxygens in the lipid headgroup and a cluster of positively charged lysine residues on the amphipathic S1 domain and the C-terminal end of the second trans-membrane helix. We take advantage of this strong interaction (estimated to be 10-13 kT per lipid) to actuate the channel (by applying forces on protein-bound lipids) and explore its sensitivity to the pulling magnitude and direction. We conclude by highlighting the simple motif that confers MscL with strong anchoring to the bilayer, and its presence in various integral membrane proteins including the human mechanosensitive channel K2P1 and bovine rhodopsin