The first records of coenagrionid damselflies (Odonata: Zygoptera: Coenagrionidae: Neoerythromma sp. and Nehalennia sp.) from Mexican Amber (Miocene)

Two specimens of the damselfly (Odonata: Zygoptera) family Coenagrionidae are described from Mexican amber of early Miocene age, identified as Neoerythromma sp. and Nehalennia sp. They constitute the first records of the family Coenagrionidae from this amber, and the first fossil records of the genera Neoerythromma and Nehalennia

Identification of novel cold-adapted nitrilase superfamily enzymes

Philosophiae Doctor - PhDIn bacteria, nitrile hydratases and enzymes of nitrilase and signature amidase superfamilies hydrolyse nitriles and amides to their corresponding carboxylic acids releasing ammonia. Bacteria expressing these enzymes are typically isolated where a sole nitrogen and/or carbon source is used to support their growth. The majority of characterised enzymes of industrial potential have been identified for their stabilities at elevated temperatures. To date, no reports of such enzymes have been isolated from cold adapted bacteria.In this study, an extensive screening program of cold-active microbial isolates for enzymes of this group led to the selection and detailed characterisation of an aliphatic amidase from Nesterenkonia.Nesterenkonia AN1, a new psychrotrophic isolate of the genus, was isolated from soil samples collected from the Miers Valley, Antarctica. AN1 showed significant 16S rRNA sequence identity to known members of the genera, but this is the only strain that had optimal growth at approximately 21oC. AN1, similar to known members, is an obligately alkaliphilic (pH 9-10) and halotolerant (Na+ 0- 15% (w/v)) strain.The genome of Nesterenkonia AN1, sequenced in-house, revealed two ORFs encoding putative nitrilases, referred to as Nit1 and Nit2. Based on analysis of their deduced protein sequences, both belonged to the nitrilase superfamily. Both sequences showed conserved catalytic residues (EKEC), glycine residues and contained the characteristic áââá monomer fold. Homology modelling using known structures suggested that both genes could encode N-carbamoyl D-amino acid amidohydrolases, although neither showed conserved residues implicated in the hydrolysis of carbamoyls.Nit1 and Nit2 were expressed in Escherichia coli BL21 (DE3) pLysS as Cterminal and N-terminal hexahistidine tagged fusion proteins, and purified using Ni-chelation chromatography. Nit1 showed no activity towards nitrile, amide and carbamoyl substrates. This protein, unlike members of the multimeric enzymes of the nitrilase superfamily, was a monomer ~30 kDa protein. It is possible that the C-terminal hexahistidine tag might have prevented Nit1 from forming multimeric proteins.Nit2 showed substrate specificity similar to known aliphatic amidases with a preference for small amides. Nit2 had maximal activity at 30oC and between pH 6.5 and 7.5, properties compatible with its cold-adapted alkaliphilic origins. In addition, the enzyme was irreversibly inactivated at temperatures above 30oC and had a half-life of approximately 7 mins at 60oC. The crystal structure of Nit2 was solved to 1.66 Å. It revealed a ~45.5 kDa dimer, composed of two tightly bound ~30 kDa monomers. These monomers associated along the A surface forming a áââá-áââá sandwich architecture that is conserved in known structures of the nitrilase superfamily.Nit2 is distinct from known aliphatic amidases in both its structure and enzymic activity: the enzyme did not possess an extended C-terminal region; is active in dimeric form; has high affinity for 3C amides rather than 2C amides; and has a low overall catalytic rate. The short C-terminal region of Nit2 may have contributed to the low stability of the enzyme at elevated temperatures. A dendrogram composed of protein sequences of members of the nitrilase superfamily and Nit2 further supported evidence that this aliphatic amidase falls within a distinct group of enzymes.This is the first report of the enzymic characterisation and structural analysis of an aliphatic amidase from a psychrotolerant, alkaliphilic and halotolerant extremophile

Development of an experimental system to investigate the interaction between the Helicoverpa armigera stunt virus capsid protein and viral RNA

Tetraviruses are entomopathogenic viruses that propagate solely in lepidopteran hosts. Viruses of this group possess non-enveloped 38- to 40-nm capsids arranged in T = 4 surface symmetry. The viral genome consists of one or two single stranded positive sense RNA strands, which define the two genera of this family, the monopartite betatetraviruses and the bipartite omegatetraviruses. Two extensively studied members of the tetraviruses are the omegatetraviruses, Helicoverpa armigera stunt virus (HaSV) and the closely related Nudaurelia capensis ω virus (NωV). The larger genomic strand of HaSV (RNA1) encodes the viral replicase, while the other (RNA2) encodes the 71-kDa capsid precursor protein (p71). The pro-capsid is assembled from 240 copies of p71, which undergo a maturation auto-catalytic cleavage into the 64-kDa (p64) capsid protein and a 7-kDa peptide (p7) forming the capsid shell. The mechanism for the recognition and packaging of the viral genome is poorly understood for these viruses. The principle objective of the research described in this study was to develop in vitro and in vivo experimental systems to investigate interactions between the N terminal domain of HaSV p71 and viral RNAs. More specifically, the two positively charged clusters of predominantly arginine residues that are conserved amongst tetraviruses and the structurally analologous nodaviruses capsid protomers’ N terminal domains were investigated. An in vitro RNA-protein “pull down” system was developed using the rapid protein purification technique of the IMPACTTM-CN system. The coding sequence of the N terminal domain of p71 was fused to that of a chitin binding affinity tag (intein). This fusion protein was used as protein bait for the viral RNA. It was proposed that if RNA interacted with the fusion protein, it would be pulled down by the mass of affinity matrix and be precipitated and fluoresce when analysed by agarose gel electrophoresis using ethidium bromide. Despite optimisation of the in vitro assay, results were affected by the interaction between the intein-tag and nucleic acids, the state of the expressed fusion protein (in particular self-cleavage) and the excessive fluorescence present on the gels. The ADH2-GAPDH yeast expression system was used to investigate the in vivo assembly of p71 containing deletions of either one or both clusters within N terminal domain. It was found that all p71 mutants were expressed with the exception of the mutant containing a deletion of the second cluster. The reasons for this still require further investigation. The expressed p71 mutants were not processed into p64 and were degraded in vivo. In addition, an experimental attempt to purify assembled p71 mutant VLPs was unsuccessful. The assembly defect of p71 mutants emphasised the significance of the clusters, which are possibly required for interaction with viral RNAs for efficient VLP assembly. The results of this study suggest that an alternative tag or in vitro RNA-protein interaction assay be used. In addition, further experiments are required to investigate whether the co-expression of full length viral RNAs are required to rescue the in vivo assembly defect of p71 mutants into VLPs

Data-Driven Decision Making in Response to the COVID-19 Pandemic: A City of Cape Town Case Study

In the event of a crisis, such as COVID-19, the decisions and subsequent actions taken by the local government are one of the primary sources of support to the local population. Yet the processes through which these decisions are reached and the data engineering advancements made for and during events are poorly reported. Understanding the capabilities and constraints in which city officials operate is essential for impactful academic research alongside global city comparison and discussion on best practices in reaching optimal and data-informed decisions. This is especially pertinent for the global South, where informality in housing and the economy presents further challenges to appropriate resource distribution in a crisis. Here, we present insights into the City of Cape Town’s data-driven response and subsequent data engineering and analytical developments throughout the COVID-19 pandemic. This is based upon a review of internal documentation including a close-out report which summarised semi-structured interviews with staff involved in the data work stream. The paper reports on the deliverables produced during 2020 by the data work stream and outlines specific challenges the city faced and its data-informed response in the areas of (1) quantifying costs for COVID-19 initiatives, (2) dealing with a surge in fatalities, (3) guiding scarce public resources to respond to an evolving crisis, and (4) data sharing. We demonstrate the real-term value of incorporating data into the decision-making process and conclude by outlining key factors that cities and researchers must consider as a part of the usual business to effectively assist their populations during times of stress and crisis

IL-4 subverts mycobacterial containment in Mycobacterium tuberculosis-infected human macrophages.

Protective immunity against Mycobacterium tuberculosis is poorly understood. The role of interleukin (IL)-4, the archetypal T-helper type 2 (Th2) cytokine, in the immunopathogenesis of human tuberculosis remains unclear.Blood and/or bronchoalveolar lavage fluid (BAL) were obtained from participants with pulmonary tuberculosis (TB) (n=23) and presumed latent TB infection (LTBI) (n=22). Messenger RNA expression levels of interferon (IFN)-γ, IL-4 and its splice variant IL-4δ2 were determined by real-time PCR. The effect of human recombinant (hr)IL-4 on mycobacterial survival/containment (CFU·mL-1) was evaluated in M. tuberculosis-infected macrophages co-cultured with mycobacterial antigen-primed effector T-cells. Regulatory T-cell (Treg) and Th1 cytokine levels were evaluated using flow cytometry.In blood, but not BAL, IL-4 mRNA levels (p=0.02) and the IL-4/IFN-γ ratio (p=0.01) was higher in TB versus LTBI. hrIL-4 reduced mycobacterial containment in infected macrophages (p<0.008) in a dose-dependent manner and was associated with an increase in Tregs (p<0.001), but decreased CD4+Th1 cytokine levels (CD4+IFN-γ+ p<0.001; CD4+TNFα+ p=0.01). Blocking IL-4 significantly neutralised mycobacterial containment (p=0.03), CD4+IFNγ+ levels (p=0.03) and Treg expression (p=0.03).IL-4 can subvert mycobacterial containment in human macrophages, probably via perturbations in Treg and Th1-linked pathways. These data may have implications for the design of effective TB vaccines and host-directed therapies

Faith seeking understanding

The debate between faith and science is an ongoing and dynamic conversation marked by the need to consistently factor in new data generated by the sciences, and new perspectives developed in theology. In this book, a group of theologians and ethicists provide insights into the debate from a faith perspective. The basic thesis permeating the discussions is that faith and science are capable of enriching and complementing each other, albeit in their own unique way. What unifies faith and science is the search for truth. What differentiates them is the unique lenses they employ to find the truth. In the end, both scientists and theologians must take into account all the pathways and lenses that lead us to a better understanding of reality. This study presents concrete examples of how theological knowledge and scientific data can be fruitfully used and integrated to develop new horizons of understanding. The general aim of this contribution was to narrow in on some of the burning themes that are driving the faith or science scholarly debate. Each contributor highlights a different aspect of the debate. The topics addressed include theoretical perspectives on the science-faith relation, the ancient scientific worldview of the creation narratives in Genesis, evolution and human origins, science and African Pentecostalism, faith and the Fourth Industrial Revolution, science and transhumanism, science and traditional medicine, and the role that faith and science can play in the human quest for meaning. Most of the contributors approach the topic from a post-foundationalist and postpositivist epistemological point of view. A wide range of hermeneutical methods is employed, ranging from systematic biblical-theological perspectives to literary and source criticism. Analytical, normative and existential philosophical arguments are also utilised throughout the course of the book. The most important contribution of the book lies in the transdisciplinary perspectives that emanate from the discussion. The ways in which the authors go about integrating theological and scientific perspectives to address ultimate questions about meaning and to inform moral discourse show that religion still has an important role to play in a world increasingly shaped by technological rationality. At the same time, it indicates that religion and science do not have to stand in conflict with each other. If the two lenses on reality engage in mature dialogue, they can enrich, inform and, on some occasions, even correct each other. The target audience of this book includes theological scholars, natural scientists and science philosophers. This book contains no plagiarism, and none of the work has been published elsewhere

Molecular characterization of Staphylococcus aureus isolates from various healthcare institutions in Nairobi, Kenya: a cross sectional study

Background: Staphylococcus aureus (S. aureus) has established itself over the years as a major cause of morbidity and mortality both within the community and in healthcare settings. Methicillin resistant S. aureus (MRSA) in particular has been a major cause of nosocomial infections resulting in significant increase in healthcare costs. In Africa, the MRSA prevalence has been shown to vary across different countries. In order to better understand the epidemiology of MRSA in a setting, it is important to define its population structure using molecular tools as different clones have been found to predominate in certain geographical locations. Methods: We carried out PFGE, MLST, SCCmec and spa typing of selected S. aureus isolates from a private and public referral hospital in Nairobi, Kenya. Results: A total of 93 S. aureus isolates were grouped into 19 PFGE clonal complexes (A–S) and 12 singletons. From these, 55 (32 MRSA and 23 MSSA) representative isolates from each PFGE clonal complex and all singletons were spa typed. There were 18 different MRSA spa types and 22 MSSA spa types. The predominant MRSA spa type was t037 comprising 40.6 % (13/32) of all MRSA. In contrast, the MSSA were quite heterogeneous, only 2 out of 23 MSSA shared the same spa type. Two new MRSA spa types (t13149 and t13150) and 3 new MSSA spa types (t13182, t13193 and t13194) were identified. The predominant clonal complex was CC 5 which included multi-locus sequence types 1, 8 and 241. Conclusion: In contrast to previous studies published from Kenya, there’s marked genetic diversity amongst clinical MRSA isolates in Nairobi including the presence of well-known epidemic MRSA clones. Given that these clones are resident within our referral hospitals, adherence to strict infection control measures needs to be ensured to reduce morbidity and mortality associated with hospital acquired MRSA infections

Faith seeking understanding

The debate between faith and science is an ongoing and dynamic conversation marked by the need to consistently factor in new data generated by the sciences, and new perspectives developed in theology. In this book, a group of theologians and ethicists provide insights into the debate from a faith perspective. The basic thesis permeating the discussions is that faith and science are capable of enriching and complementing each other, albeit in their own unique way. What unifies faith and science is the search for truth. What differentiates them is the unique lenses they employ to find the truth. In the end, both scientists and theologians must take into account all the pathways and lenses that lead us to a better understanding of reality. This study presents concrete examples of how theological knowledge and scientific data can be fruitfully used and integrated to develop new horizons of understanding. The general aim of this contribution was to narrow in on some of the burning themes that are driving the faith or science scholarly debate. Each contributor highlights a different aspect of the debate. The topics addressed include theoretical perspectives on the science-faith relation, the ancient scientific worldview of the creation narratives in Genesis, evolution and human origins, science and African Pentecostalism, faith and the Fourth Industrial Revolution, science and transhumanism, science and traditional medicine, and the role that faith and science can play in the human quest for meaning. Most of the contributors approach the topic from a post-foundationalist and postpositivist epistemological point of view. A wide range of hermeneutical methods is employed, ranging from systematic biblical-theological perspectives to literary and source criticism. Analytical, normative and existential philosophical arguments are also utilised throughout the course of the book. The most important contribution of the book lies in the transdisciplinary perspectives that emanate from the discussion. The ways in which the authors go about integrating theological and scientific perspectives to address ultimate questions about meaning and to inform moral discourse show that religion still has an important role to play in a world increasingly shaped by technological rationality. At the same time, it indicates that religion and science do not have to stand in conflict with each other. If the two lenses on reality engage in mature dialogue, they can enrich, inform and, on some occasions, even correct each other. The target audience of this book includes theological scholars, natural scientists and science philosophers. This book contains no plagiarism, and none of the work has been published elsewhere

Contraceptive Preference Among Women at Risk of HIV Acquisition in a Preparatory Screening Study for a Phase III Microbicide Trial in South Western Uganda.

Contraceptive preferences of women at risk for HIV acquisition are not well documented. We report on contraceptive choices among women residing in small townships in southwestern Uganda. This was part of preparatory efforts for recruitment into the Ring Study, a phase 3 microbicide trial, between July 2013 and October 2014. Clinicians provided contraceptives per a woman's choice. HIV testing and screening for other sexually transmitted infections were done at first contact and at screening for the trial. Contraceptive choice was summarized by demographics and regression analysis to show factors associated with use of the injectable method. Of 6725 women contacted, 489 were prescreened. Of these 489 women, most (306, 63%) were already using contraception. Injectables were most preferred (58.7%), followed by implants (23.9%). Women living with a regular sexual partner preferred the injectable method (61.0%, P = 0.06), compared with other methods. Women at risk for HIV infection are willing to initiate use of modern contraceptives, which may reduce study dropout during intervention trials due to unintended pregnancy. Registration no: NCT01539226