Improving Nutrition through Agriculture : Viewing agriculture-nutrition linkages along the smallholder value chain

This report is a synthesis of existing global knowledge on improving nutrition through agriculture using a smallholder value chain approach. The smallholder value chain model used by the desk review concentrates on both producers and consumers and is centred around three pathways: improved nutrition resulting from increased production for own consumption, improved nutrition through increased income from selling agricultural products, and improved nutrition through increased income resulting from farmers’ involvement in local or regional procurement programs. The report identifies key conditions for agricultural interventions to significantly contribute to nutrition as well as important knowledge gaps pertaining to agriculture-nutrition linkages

Destructive sampling natural science collections: an overview for museum professionals and researchers

There are many reasons why museum collections may be used for destructive sampling, from DNA and isotope analysis to radiocarbon dating. The process is invasive and destroys a part, or all, of the specimen. This can result in reluctance by museum staff to allow specimens to be used in particular types of scientific research. We will present some of the motivations on both sides, but argue that the benefits of destructive sampling can outweigh the risks. Many analytical methods have improved dramatically in the last 30 years, requiring smaller sample sizes. With a focus on destructive sampling for genetic analysis, we will also present some examples from the literature where DNA from museum and archaeological specimens has greatly aided the reconstruction of a species' evolutionary history as well as enriching our understanding of the object sampled. In addition, we highlight the need for museum staff to understand exactly what researchers are asking for, and for researchers in turn to understand museum procedures. We include an example of a Destructive Sampling Policy and a Destructive Sampling Request Form, for institutions to adapt for their own use

Human Dispersal Out of Africa: A Lasting Debate

Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings

Destructive sampling natural science collections: an overview for museum professionals and researchers

There are many reasons why museum collections may be used for destructive sampling, from DNA and isotope analysis to radiocarbon dating. The process is invasive and destroys a part, or all, of the specimen. This can result in reluctance by museum staff to allow specimens to be used in particular types of scientific research. We will present some of the motivations on both sides, but argue that the benefits of destructive sampling can outweigh the risks. Many analytical methods have improved dramatically in the last 30 years, requiring smaller sample sizes. With a focus on destructive sampling for genetic analysis, we will also present some examples from the literature where DNA from museum and archaeological specimens has greatly aided the reconstruction of a species' evolutionary history as well as enriching our understanding of the object sampled. In addition, we highlight the need for museum staff to understand exactly what researchers are asking for, and for researchers in turn to understand museum procedures. We include an example of a Destructive Sampling Policy and a Destructive Sampling Request Form, for institutions to adapt for their own use

Forward Signaling by Unipolar Brush Cells in the Mouse Cerebellum

Unipolar brush cells (UBCs) are glutamatergic interneurons prominently present in the granular layer of the vestibulocerebellum. UBCs engage in extensive synaptic contact with a single presynaptic mossy fiber and signal to downstream granule cells through an elaborate network of mossy fiber-like axons. Ultrastructural examinations and electrophysiological recordings in organotypic slice cultures have indicated that UBCs target not only granule cells but also other UBCs, thus forming chains of two or perhaps more interconnected UBCs. In this report, we show recordings of spontaneous and evoked (di)synaptic events in granule cells and UBCs in fresh cerebellar slices from juvenile mice (5–7 weeks). The patterns of arrival of synaptic events were consistent with the presence of a presynaptic UBC, and recordings from UBCs displayed spontaneous protracted synaptic events characteristic of UBC excitatory synaptic transmission. These results highlight that chains of UBCs could further extend the temporal range of delayed and protracted signaling in the cerebellar cortical network

Excitation and Excitability of Unipolar Brush Cells

__Abstract__ The cerebellum is a distinct brain structure that ensures the spatial accuracy and temporal coordination of movements. It is located superimposed on the brainstem and has an appearance and organization unlike that of the cerebral cortex: its surface has a highly regular foliation pattern, and its neural circuitry is organized in repeated structured modules. Neural activity enters the cerebellum via two excitatory pathways, the mossy ber system and the climbing ber system. Climbing bers originate from the inferior olivary nucleus in the brainstem, and assert a powerful in uence on cerebellar output and long-term adaptation processes. Mossy bers originate from a large number of sources, and carry contextual information on sensory inputs, aspects of motor planning and commands, and proprioceptive feedback. In the cerebellum this information is evaluated and integrated, to produce neural output that in uences ongoing movement directly. Mossy ber signals are processed in the cerebellum in three stages. In the granular layer, the input stage of the cerebellum, mossy ber signals undergo a recoding step where they are combined and expanded by granule cells. Next, in the molecular layer, granule cell signals are integrated with climbing ber signals in Purkinje cells. Together, the granular la

Agriculture-nutrition linkages : Linking agriculture and food security to nutrition improvement

The literature review explores possibilities to include nutritional considerations into policies and programmes in the field of agriculture, value chain development and food security. Rationale for the literature review is the renewed attention for agriculture and nutrition on international agenda’s and more specifically the renewed attention on linking the two: how can interventions in agriculture contribute to improvements in the nutritional situation, and under what conditions

Estimating entropies from molecular dynamics simulations

The methods to compute the excess entropy and the entropy of solvation using liquid water as a test system were studied. The accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated. Through the thermodynamic integration accurate entropy differences were obtained in which many copies of a solute were desolvated. Only two methods yield useful results, the calculation of solute-solvent entropy through thermodynamic integration and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference, when one solute molecule is involved

Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

The Ari peoples of Ethiopia are comprised of different occupational groups that can be distinguished genetically, with Ari Cultivators and the socially marginalised Ari Blacksmiths recently shown to have a similar level of genetic differentiation between them (FST ≈ 0.023 - 0.04) as that observed among multiple ethnic groups sampled throughout Ethiopia. Anthropologists have proposed two competing theories to explain the origins of the Ari Blacksmiths as (i) remnants of a population that inhabited Ethiopia prior to the arrival of agriculturists (e.g. Cultivators), or (ii) relatively recently related to the Cultivators but presently marginalized in the community due to their trade. Two recent studies by different groups analysed genome-wide DNA from samples of Ari Blacksmiths and Cultivators and suggested that genetic patterns between the two groups were more consistent with model (i) and subsequent assimilation of the indigenous peoples into the expanding agriculturalist community. We analysed the same samples using approaches designed to attenuate signals of genetic differentiation that are attributable to allelic drift within a population. By doing so, we provide evidence that the genetic differences between Ari Blacksmiths and Cultivators can be entirely explained by bottleneck effects consistent with hypothesis (ii). This finding serves as both a cautionary tale about interpreting results from unsupervised clustering algorithms, and suggests that social constructions are contributing directly to genetic differentiation over a relatively short time period among previously genetically similar groups

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study.

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results. Few published comparisons exist for the myriad analytical pipelines used for predicting AMR. To address this, we performed an inter-laboratory study providing sets of participating researchers with identical short-read WGS data from clinical isolates, allowing us to assess the reproducibility of the bioinformatic prediction of AMR between participants, and identify problem cases and factors that lead to discordant results. We produced ten WGS datasets of varying quality from cultured carbapenem-resistant organisms obtained from clinical samples sequenced on either an Illumina NextSeq or HiSeq instrument. Nine participating teams ('participants') were provided these sequence data without any other contextual information. Each participant used their choice of pipeline to determine the species, the presence of resistance-associated genes, and to predict susceptibility or resistance to amikacin, gentamicin, ciprofloxacin and cefotaxime. We found participants predicted different numbers of AMR-associated genes and different gene variants from the same clinical samples. The quality of the sequence data, choice of bioinformatic pipeline and interpretation of the results all contributed to discordance between participants. Although much of the inaccurate gene variant annotation did not affect genotypic resistance predictions, we observed low specificity when compared to phenotypic AST results, but this improved in samples with higher read depths. Had the results been used to predict AST and guide treatment, a different antibiotic would have been recommended for each isolate by at least one participant. These challenges, at the final analytical stage of using WGS to predict AMR, suggest the need for refinements when using this technology in clinical settings. Comprehensive public resistance sequence databases, full recommendations on sequence data quality and standardization in the comparisons between genotype and resistance phenotypes will all play a fundamental role in the successful implementation of AST prediction using WGS in clinical microbiology laboratories