Developmental and environmental induction of Lea and LeaA mRNAs and the postabscission program during embryo culture.

The major programs of gene expression during late embryogenesis are the muturation or reserve accumulation program and, after ovule abscission, the postabscission program that is composed largely of Lea and LeaA mRNAs that probably encode desiccation protectants. There are diverse opinions about the developmental regulators of these programs. Several candidates are evaluated here by measuring, in cultured embryos, the accumulation kinetics of cloned mRNAs specifically expressed in the normal maturation, postabscission, or germination programs of cotton. Maturation-stage embryos both terminate the maturation program and induce the postabscission program after excision and culture, just as they do later in the plant after ovule abscission. However, they also induce simultaneously the germination program and are thus different from any normal stage of embryo development or germination. The developmental induction of the postabscission program in culture does not require exogenous abscisic acid, but its expression is enhanced by precocious desiccation or culture on abscisic acid or high osmoticum, probably by an environmentally responsive mechanism that normally operates during germination. Normal desiccation does not control any of these programs because the embryo acquires all of the characteristics of a mature embryo before it desiccates. These and other results suggest regulation of normal embryogenesis by a maternal maturation factor, a postabscission factor, and the postabscission program.     

Global agricultural intensification during climate change: a role for genomics

Agriculture is now facing the ‘perfect storm’ of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic‐assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.     

Comparative High-Density Microarray Analysis of Gene Expression during Growth of Lactobacillus helveticus in Milk versus Rich Culture Medium

Lactobacillus helveticus CNRZ32 is used by the dairy industry to modulate cheese flavor. The compilation of a draft genome sequence for this strain allowed us to identify and completely sequence 168 genes potentially important for the growth of this organism in milk or for cheese flavor development. The primary aim of this study was to investigate the expression of these genes during growth in milk and MRS medium by using microarrays. Oligonucleotide probes against each of the completely sequenced genes were compiled on maskless photolithography-based DNA microarrays. Additionally, the entire draft genome sequence was used to produce tiled microarrays in which noninterrupted sequence contigs were covered by consecutive 24-mer probes and associated mismatch probe sets. Total RNA isolated from cells grown in skim milk or in MRS to mid-log phase was used as a template to synthesize cDNA, followed by Cy3 labeling and hybridization. An analysis of data from annotated gene probes identified 42 genes that were upregulated during the growth of CNRZ32 in milk (P < 0.05), and 25 of these genes showed upregulation after applying Bonferroni's adjustment. The tiled microarrays identified numerous additional genes that were upregulated in milk versus MRS. Collectively, array data showed the growth of CNRZ32 in milk-induced genes encoding cell-envelope proteinases, oligopeptide transporters, and endopeptidases as well as enzymes for lactose and cysteine pathways, de novo synthesis, and/or salvage pathways for purines and pyrimidines and other functions. Genes for a hypothetical phosphoserine utilization pathway were also differentially expressed. Preliminary experiments indicate that cheese-derived, phosphoserine-containing peptides increase growth rates of CNRZ32 in a chemically defined medium. These results suggest that phosphoserine is used as an energy source during the growth of L. helveticus CNRZ32.     

Using a bistable animal opsin for switchable and scalable optogenetic inhibition of neurons

There is no consensus on the best inhibitory optogenetic tool. Since Gi/o signalling is a native mechanism of neuronal inhibition, we asked whether Lamprey Parapinopsin (“Lamplight”), a Gi/o‐coupled bistable animal opsin, could be used for optogenetic silencing. We show that short (405 nm) and long (525 nm) wavelength pulses repeatedly switch Lamplight between stable signalling active and inactive states, respectively, and that combining these wavelengths can be used to achieve intermediate levels of activity. These properties can be applied to produce switchable neuronal hyperpolarisation and suppression of spontaneous spike firing in the mouse hypothalamic suprachiasmatic nucleus. Expressing Lamplight in (predominantly) ON bipolar cells can photosensitise retinas following advanced photoreceptor degeneration, with 405 and 525 nm stimuli producing responses of opposite sign in the output neurons of the retina. We conclude that bistable animal opsins can co‐opt endogenous signalling mechanisms to allow optogenetic inhibition that is scalable, sustained and reversible.     

Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 15,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 395,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, but modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 7 specific genes, and by clonal expansion. Clones in which a provirus integrated in an oncogene contributed to cell survival comprised only a small fraction of the clones persisting in on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist.     

Does the heterogeneity of autism undermine the neurodiversity paradigm?

The neurodiversity paradigm is presented by its proponents as providing a philosophical foundation for the activism of the neurodiversity movement. Its central claims are that autism and other neurodivergent conditions are not disorders because they are not intrinsically harmful, and that they are valuable, natural and/or normal parts of human neurocognitive variation. This paper: (a) identifies the non‐disorder claim as the most central of these, based on its prominence in the literature and connections with the practical policy claims that the paradigm is supposed to support; (b) describes the heterogeneity of autism at the behavioural and causal levels, and argues that at the behavioural level this encompasses ways of being autistic that are harmful in ways that cannot be not wholly attributed to discrimination or unjust social arrangements, challenging the claim that autism is not a disorder; (c) considers and rejects responses to this challenge based on separation of high‐ and low‐functioning autism, separation of autism from co‐occurring conditions, and viewing autism as part of an individual’s identity. Two of these responses fail for reasons that are themselves connected with the behavioural and/or causal heterogeneity of autism.     

Microbial single-strand annealing proteins enable CRISPR gene-editing tools with improved knock-in efficiencies and reduced off-target effects

Several existing technologies enable short genomic alterations including generating indels and short nucleotide variants, however, engineering more significant genomic changes is more challenging due to reduced efficiency and precision. Here, we developed RecT Editor via Designer-Cas9-Initiated Targeting (REDIT), which leverages phage single-stranded DNA-annealing proteins (SSAP) RecT for mammalian genome engineering. Relative to Cas9-mediated homology-directed repair (HDR), REDIT yielded up to a 5-fold increase of efficiency to insert kilobase-scale exogenous sequences at defined genomic regions. We validated our REDIT approach using different formats and lengths of knock-in templates. We further demonstrated that REDIT tools using Cas9 nickase have efficient gene-editing activities and reduced off-target errors, measured using a combination of targeted sequencing, genome-wide indel, and insertion mapping assays. Our experiments inhibiting repair enzyme activities suggested that REDIT has the potential to overcome limitations of endogenous DNA repair steps. Finally, our REDIT method is applicable across cell types including human stem cells, and is generalizable to different Cas9 enzymes.     

Evaluation of Changes in Equine Care and Limb-Related Abnormalities in Working Horses in Jaipur,India, as Part of a Two Year Participatory Intervention Study

BackgroundPrevious studies have found the prevalence of lameness in working horses to be 90–100%. Risk factors for lameness in this important equine population, together with risk-reduction strategies adopted by their owners, are poorly understood. The objective was to uncover risk factors for lameness and limb abnormalities in working horses, by associating clinical lameness examination findings on three occasions over two years with owner reported changes in equine management and work practices over this period.Conclusions/SignificanceThis study illustrates the complexity and interacting nature of risk factors for lameness in working horses, and highlights the importance of longitudinal investigations that recognise and address this. PI group owners found the project useful and requested similar inputs in future. Our findings demonstrate the value of exploratory and participatory research methodology in the field of working horse welfare.