An investigation of the effects of stage of ensilage on Nassella neesiana seeds, for reducing seed viability and injury to livestock

The noxious weed Nassella neesiana is established on a wide range of productive land throughout southeastern Australia. N. neesiana seeds, when mature, are sharp, causing injury to livestock, thus posing a problem in fodder bales. To reduce infestations of agricultural weeds in situ, production of silage from weed-infested pastures is practised as part of integrated weed management (IWM). However, there is little data to demonstrate whether this process is useful to reduce infestations or the harmful properties of N. neesiana. Therefore, the minimum duration of ensilage required to reduce the viability of N. neesiana seeds was investigated, both with and without addition of ensilage inoculants in this process. Also, the decreasing propensity of the seeds to injure livestock, after various times and conditions of ensilage, was assessed. Ensilage inoculant reduced seed germination probability to zero after 35 days. When no inoculant was added, zero viability was achieved after 42 days. A qualitative assessment of the hardness of ensilaged seeds found seed husks were softer (and therefore safer) after 42 days, whether inoculant was used or not. Therefore, we suggest that both the viability of N. neesiana seeds and hardness of seed casings are significantly reduced after 42 days, thereby reducing the risks of seed dispersal and injury to livestock

Changing women's roles, changing environmental knowledges: evidence from Upper Egypt

The aim of this paper is to investigate the ways in which changing gender roles in a Bedouin community in Upper Egypt, brought about by settlement over the last 20 years on the shores of Lake Nasser, have impacted on the accumulation and development of indigenous environmental knowledges by Bedouin women. The research was carried out among four groups of Ababda Bedouin in the Eastern Desert of Egypt and involved in-depth monthly conversations carried out over a period of 12 months. The main conclusions of the study are that the women of the study area have had to develop new knowledges which, in some cases, are now different from those held by men because of the different economic circumstances in which many find themselves; that these knowledges are fluid, dynamic and ever-changing with their own internal dynamism; and that socially constructed notions of gender are vital in the development process, notions that are sensitive to both men's and women's interests and their interrelationships

KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units

Protein kinases are important targets for treating human disorders, and they are the second most targeted families after G-protein coupled receptors. Several resources provide classification of kinases into evolutionary families (based on sequence homology); however, very few systematically classify functional families (FunFams) comprising evolutionary relatives that share similar functional properties. We have developed the FunFam-MARC (Multidomain ARchitecture-based Clustering) protocol, which uses multi-domain architectures of protein kinases and specificity-determining residues for functional family classification. FunFam-MARC predicts 2210 kinase functional families (KinFams), which have increased functional coherence, in terms of EC annotations, compared to the widely used KinBase classification. Our protocol provides a comprehensive classification for kinase sequences from >10,000 organisms. We associate human KinFams with diseases and drugs and identify 28 druggable human KinFams, i.e., enriched in clinically approved drugs. Since relatives in the same druggable KinFam tend to be structurally conserved, including the drug-binding site, these KinFams may be valuable for shortlisting therapeutic targets. Information on the human KinFams and associated 3D structures from AlphaFold2 are provided via our CATH FTP website and Zenodo. This gives the domain structure representative of each KinFam together with information on any drug compounds available. For 32% of the KinFams, we provide information on highly conserved residue sites that may be associated with specificity.Adeyelu T, Bordin N, Waman VP, Sadlej M, Sillitoe I, Moya-Garcia AA, Orengo CA. KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units. Biomolecules. 2023; 13(2):277. https://doi.org/10.3390/biom1302027

Midlands Cadences: Narrative Voices in the Work of Alan Sillitoe

This paper will examine excerpts from a range of Alan Sillitoe’s prose fiction, most notably Saturday Night and Sunday Morning (1958) and short stories from the collection The Loneliness of the Long-Distance Runner (1958), via a comparative exploration of the texts’ representations of Midlands English demotic. Both texts enact Bakhtin’s notion of novelistic dialogism and find much expressive capital in the tension between discourses: between the oral and the written. Indeed, it could be argued that much of Sillitoe’s work functions as a direct challenge to dominant notions of the literary. The narrative discourse attempts to trace a link between the quotidian experience of the Midlands English working classes represented and the demotic language which they speak. His technique also explores the link between language and sensibility; i.e. verbal articulacy need not be a limit to expression of a character’s distinctive identity. In contrast to the more radical techniques of novelists like James Kelman and Irvine Welsh, all instances of phonetically-rendered demotic remain imprisoned by what Joyce called ‘perverted commas’ – as direct speech. However, the diegetic narrative discourse itself is redolent of registers rooted in 1950s English working class life. The texts also contain different methods of representing their protagonists’ consciousness through their own idiolect. In Saturday Night and Sunday Morning, this is evidenced by the use of the second person ‘you’. It functions simultaneously as a representation of Seaton’s consciousness in the oral register which he might choose to articulate it, and as a dialogic ‘sideways glance’ at the reader and assumed shared experience. The second is more redolent of internal monologue, using the first-person form (as seen in the homodiegetic narration of the second novel); crucially, though, it remains in Standard English, if explicitly orientated towards oral register. Sillitoe’s is a novelistic discourse which refuses to normalise itself to accord with the conventions of classic realism, and as such prefigures the ambitions of many contemporary writers who incline their narrative voices towards the oral – asserting the right of a character’s dialect/idiolect to be the principal register of the narrative. The paper will demonstrate this thesis through the ideas of Bakhtin, and through an analytical taxonomy derived from literary stylistics. It aims to propose a model which can be used to analyse and explore any fiction which has been labelled as ‘working class’, and asserts that such an approach leads to a more principled characterisation of working class fiction (based on its use of language) than current literary-critical discussions based simply on cultural/social context and biography

Indigenous knowledges and development: a postcolonial caution

As a result of the failure of formal top-down development, there has recently been increased interest in the possibilities of drawing upon the indigenous knowledges of those in the communities involved, in an attempt to produce more effective development strategies. The concept of indigenous knowledge calls for the inclusion of local voices and priorities, and promises empowerment through ownership of the process. However, there has been little critical examination of the ways in which indigenous knowledges have been included in the development process. Drawing upon postcolonial theory, this article suggests that indigenous knowledges are often drawn into development by both theorists and development institutions in a very limited way, failing to engage with other ways of perceiving development, and thus missing the possibility of devising more challenging alternatives

Abnormal dysbindin expression in cerebellar mossy fiber synapses in the mdx mouse model of Duchenne muscular dystrophy

The dystrophin-associated protein complex (DPC), comprising sarcoglycans, dystroglycans, dystrobrevins, and syntrophins, is a component of synapses both in muscle and brain. Dysbindin is a novel component of the DPC, which binds to β-dystrobrevin and may serve as an adaptor protein that links the DPC to an intracellular signaling cascade. Disruption of the DPC results in muscular dystrophy, and mutations in the human ortholog of dysbindin have been implicated in the pathogenesis of schizophrenia. In both cases, patients also present with neurological symptoms reminiscent of cerebellar problems. In the mouse cerebellum, dysbindin immunoreactivity is expressed at high levels in a subset of mossy fiber synaptic glomeruli in the granular layer. Lower levels of dysbindin immunoreactivity are also detected in Purkinje cell dendrites. In the cerebellar vermis, dysbindin-immunoreactive glomeruli are restricted to an array of parasagittal stripes that bears a consistent relationship to Purkinje cell parasagittal band boundaries as defined by the expression of the respiratory isoenzyme zebrin II/aldolase c. In a mouse model of Duchenne muscular dystrophy, the mdx mutant, in which dystrophin is not expressed, there is a dramatic increase in the number of dysbindin-immunoreactive glomeruli in the posterior cerebellar vermis. Moreover, the topography of the terminal fields is disrupted, replacing the stripes by a homogeneous distribution. Abnormal synaptic organization in the cerebellum may contribute to the neurological problems associated with muscular dystrophy and schizophrenia

The use of indigenous knowledge in development: problems and challenges

The use of indigenous knowledge has been seen by many as an alternative way of promoting development in poor rural communities in many parts of the world. By reviewing much of the recent work on indigenous knowledge, the paper suggests that a number of problems and tensions has resulted in indigenous knowledge not being as useful as hoped for or supposed. These include problems emanating from a focus on the (arte)factual; binary tensions between western science and indigenous knowledge systems; the problem of differentiation and power relations; the romanticization of indigenous knowledge; and the all too frequent decontextualization of indigenous knowledge

‘Ethnic group’, the state and the politics of representation

The assertion, even if only by implication, that ‘ethnic group’ categories represent ‘real’ tangible entities, indeed identities, is commonplace not only in the realms of political and policy discourse but also amongst contemporary social scientists. This paper, following Brubaker (2002), questions this position in a number of key respects: of these three issues will dominate the discussion that follows. First, there is an interrogation of the proposition that those to whom the categories/labels refer constitute sociologically meaningful ‘groups’ as distinct from (mere) human collectivities. Secondly, there is the question of how these categories emerge, i.e. exactly what series of events, negotiations and contestations lie behind their construction and social acceptance. Thirdly, and as a corollary to the latter point, we explore the process of reification that leads to these categories being seen to represent ‘real things in the world’ (ibid.)

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies

FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering ∼1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree

CATH: comprehensive structural and functional annotations for genome sequences.

The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235,000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant improvements to the predictive power of our functional families (FunFams); the release of our 'current' putative domain assignments (CATH-B); a new, strictly non-redundant data set of CATH domains suitable for homology benchmarking experiments (CATH-40) and a number of improvements to the web pages