microPublication biology最新文献

Neurogenic differentiation factor 2, encoded by the NEUROD2 gene, is a proneural transcription factor required for neuronal differentiation and survival. Haploinsufficiency of NEUROD2 can cause neurodevelopmental disorders with or without seizures in human infants and causes spontaneous seizures in Xenopus tadpoles. We compared transcriptomes of whole brains dissected from F ₀ neurod2 ^-/- (mosaic) stage NF47 Xenopus laevis tadpoles to those of control siblings. neurod2 knockdown increased expression of cell cycle-associated genes and decreased nerve growth factor (NGF) and chromatin modifying genes. Our results suggest Neurod2 deficiency prevents neural progenitor cells exiting the cell cycle and differentiating, predisposing the brain to hyper-excitability.

In yeast, the mitochondrial voltage-dependent anion channel (VDAC) proteins Por1 and Por2 play regulatory roles in the regulation of Snf1, an ortholog of AMP-activated protein kinase (AMPK). An important question is whether Por1 and Por2 serve as Snf1-coupled energy sensors. VDACs are β-barrel proteins, but they have a flexibly-linked N-terminal α helix (NAH) domain, suggesting a possible role in Snf1 signaling. Here, we asked whether the NAH domain of Por2 is required for promoting Snf1 nuclear translocation. In our experimental setup, the Por2 NAH was dispensable. Further experiments are required to fully understand the regulatory roles of the Por1/2 NAH domains.

Microtubule dynamics influence neuron morphogenesis. We investigated the role of the conserved microtubule-associated protein Mini Spindles (Msps) in the morphogenesis of branched dendrite arbors using Drosophila melanogaster larval class III and class IV dendritic arborization neurons as two models of branch organization. In both classes, knocking down msps expression reduced dendrite branching but increased terminal dendrite length. In msps ^RNAi class IV da neurons, dendrite growth failed to scale in proportion to increasing larval size between the second and third instar. These results suggest that Msps is required for the dynamic expansion of dendrite arbors during periods of rapid organismal growth.

Pairwise alignments (PWAs) are commonly used to compare sequences to a reference. Existing alignment tools provide algorithms to align multiple sequences to a single reference and to merge two sets of aligned sequences; but not to combine individually aligned PWAs with a common reference into a single MSA which preserves their original alignment structure. This is required for certain workflows. One example is aligning multiple sequencing traces with a circular plasmid sequence for validation. Some alignment tools that take into account the circularity of the plasmid sequence return a PWA per sequencing trace. For visualization, all PWAs have to be combined into a single MSA. For this purpose, we developed an algorithm that combines alignments sharing the same reference into an MSA, and implemented it as a classmethod in Biopython's Alignment class.

Endoreplication drives polyploidy in metabolically active epithelial tissues. Here we show that loss of Drosophila Tau increases nuclear size and DAPI fluorescence in principal and stellate cells of the Malpighian tubule, indicative of elevated DNA content. A similar increase is observed in the salivary gland, another polyploid tissue. These findings reveal a previously unrecognized role for Tau in restraining endoreplication in non-neuronal epithelia.

The increasing quantity of time-series images presents new opportunities for extracting biological insights from data. Here, we introduce a deep learning framework with a variable input sequence length to predict cell and colony morphologies. We apply this framework to in silico and in vitro microscopy datasets, evaluating the impact of temporal data on performance. We find that while performance increases monotonically with increasing in silico training data, performance is varied in the in vitro case studies. The varying results reflect the intrinsic challenges stochastic, complex biological systems pose to data-driven modeling, and offer a new method through which we can identify biological transition points using temporal dynamics.

We investigated drought growth responses in Medicago lupulina using PEG to simulate drought stress. We grew Medicago lupulina plants inoculated with Sinorhizobium meliloti in Magenta boxes under randomly assigned treatments: a control, PEG applied to the bottom (PEG added to the bottom-watering container), or PEG applied from the top (PEG poured over the growth media). PEG treatments significantly reduced above-ground growth but unexpectedly increased nodulation. Our results suggest that while PEG effectively simulates drought stress on above-ground growth parameters, it may not accurately simulate drought effects on rhizobial symbiosis.

Brewers have domesticated many strains of Saccharomyces cerevisiae with traits complementary to different beers, but these strains may also harbor undesirable characteristics. One example is the mother-daughter separation defect (MDSD) which is present in London Ale III, a popular brewing strain, and causes cells to form large clusters. MDSDs can be caused by mutations to several genes, making targeted genetic approaches to reduce MDSDs challenging. We passaged three populations for over 200 generations to generate strains with reduced MDSD, demonstrating how experimental evolution can be used to select against undesirable traits in industrial yeast strains.

Plants adjust reproductive allocation in response to environmental changes to maximize fitness. As sea level rise increases salinity in coastal forests, we examined its effects on seed rain in two tree species. Pinus taeda showed a median 52% reduction relative investment in pine cone production in high-salinity areas relative to low salinity areas. Juniperus virginiana decreased relative investment in seed production by 64%, though with higher uncertainty. These results reveal that salinity stress reduces tree allocation to reproduction in coastal forests, and suggests species-specific reproductive responses to environmental change, with implications for coastal forest dynamics under rising salinity.

Bacteriophages Bouchard and Windest are siphoviruses isolated using Arthrobacter globiformis B-2979-SEA. The genome of Bouchard is predicted to encode 91 proteins within its 57,304 bp genome, whereas the genome of Windest is predicted to encode 99 proteins and two tRNAs within its 51,773 bp genome. Based on gene content similarity of at least 35% to actinobacteriophages, Bouchard and Windest have been assigned to the AU2 subcluster and AY cluster of Actinobacteriophages, respectively.