Trending Papers in developmental biology

Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIP-on-chip data are available. However, a NCA scheme is not applicable to many biological studies due to limited topology information available, such as lack of ChIP-on-chip data. We propose a new approach, motif-directed NCA (mNCA), to integrate motif information and gene expression data to infer regulatory networks.

Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes often exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of genes with each other and with their external environments. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions. Here, we use pan-reactomes as proxies for pan-genomes since they can explicitly represent the interactions between the genes that code for metabolic reactions and simulate complex phenotypes that interact with the metabolic environment. We interpreted pan-reactomes as dynamic pools of metabolic reactions that are potentially gained or lost and simulated the routes along which different lineages lose reactions in alternative environments. We performed these simulations on the pan-reactomes of 46 bacterial and archaeal families covering a broad taxonomic range. These simulations allowed us to disentangle metabolic reactions whose presence does, and does not depend on the metabolite composition of the external environment, allowing us to identify reactions constrained “by nutrition” and “by nature”, respectively. By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages in their evolutionary past. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets. Together, we introduce a computational framework for analyzing and interpreting pan-reactomes that provides new insights into the ecological and evolutionary drivers of pan-genome composition.

The emergence of multicellularity is a key event in the evolution of life and is an attractive challenge among researchers, including those investigating the artificial design of cellular behavior . Multicellular organisms are widely distributed on Earth, and retracing the specific conditions conducive for the initial transition from unicellularity to multicellularity is difficult. However, by examining organisms that inhabit unique (e.g., isolated) environmental niches, we may be able to get a glimpse into primitive multicellularity in the context of a given environment. Here we report the discovery of a new bacterium that displayed multicellular-like characteristics and behavior. The bacterium, which was isolated adjacent to an underground stream in a limestone cave, is to be named sp. nov. HS-3. On a solid surface, HS-3 self-organizes its filamentous cells to form an appearance similar to the nematic phase of a liquid crystal . Mature colonies produce and accommodate clusters of coccobacillus progeny, and release them upon contact with water. HS-3 demonstrated novel, spatiotemporally regulated multicellularity that can resolve the so-called ‘competition-dispersal trade-off’ problem . This study illustrates a hypothetical missing link on the emergence of multicellularity.

Understanding the mechanisms that underlie chromosome evolution may provide insights into the processes underpinning the origin, persistence, and evolutionary tempo of lineages. Here we present the first database of chromosome counts for animals (the Animal Chromosome Count database, ACC) summarizing chromosome numbers for ∼18,000 species. We found remarkable similarity in the distribution of chromosome counts between animals and flowering plants. At larger timescales, selection towards a specific range might explain the similar distribution of chromosome counts between these two groups. Nevertheless, changes in chromosome number are still potential drivers of divergence among species at shorter timescales. We also found that while animals and plants exhibit similar frequencies of speciation-related changes in chromosome number, plant speciation is more often related to changes in ploidy. Based on the ACC, our analyses suggest that changes in chromosome number alone could help explain patterns of diversity within animal clades.

Globally, at the rate of 1-2 percent per annum, mangrove coverings are disappearing and 35 percent have been lost in the last 20 years due to changes in climate and human activities. No mangrove-associated crabs were found when the mangroves were artificially transplanted 25 years ago in the Vellar estuary. This mangrove ecosystem was sampled for brachyuran biodiversity estimation, species abundance, composition and evaluation of the effectiveness of DNA barcoding in brachyuran crabs species identification. A total of 2844 crabs were collected, representing 35 species within 8 families belonging to 20 genera. Four brachyuran crab species, that is, , and account for >70% of the total abundance. An approximate 87.5% of crab species estimated to occur by various species estimator were recovered in the present study. Between and , the maximum association index value was observed (97.7%). Cluster analysis grouped the sampled stations according to the types of mangrove species, clearly influencing the structure and composition of the brachyuran crabs. In general, vegetative cover composed of multiple species of mangroves is preferred for the abundance of all collected crabs species, and particularly . Analysis of DNA barcoding indicates that 40% of the brachyuran species gathered in this sample were first barcoded. The advent of new high-throughput sequencing technologies will change biomonitoring applications and surveys drastically in the near future, making reference datasets like ours relevant.

Noise impairs signal perception and is a major source of selection on animal communication. Identifying adaptations that enable receivers to cope with noise is critical to discovering how animal sensory and communication systems evolve. We integrated biophysical and bioacoustic measurements with physiological modeling to demonstrate that the lungs of frogs serve a heretofore unknown noise-control function in vocal communication. Lung resonance enhances the signal-to-noise ratio for communication by selectively reducing the tympanum’s sensitivity at critical frequencies where the tuning of two inner ear organs overlaps. Social network analysis of citizen-science data on frog calling behavior indicates the calls of other frog species in multi-species choruses are a prominent source of environmental noise attenuated by the lungs. These data reveal that an ancient adaptation for detecting sound via the lungs has been evolutionarily co-opted to create spectral contrast enhancement that contributes to solving a multi-species cocktail party problem.

Identification and quantification of fish diet diversity was the first step in understanding the food web dynamics and ecosystem energetics, where the contribution of DNA barcoding technique has been important. We used DNA barcoding to identify the stomach contents of a euryhaline, benthophagous catfish . From 40 catfish stomach items sampled in two different seasons, we barcoded 67 piscine and macro-invertebrates prey items, identified as belonging to 13 species in 4 major phyla (viz., Chordate, Arthropod, Annelida and Mollusca). It is important to note that the mollusc taxa and and a species of fish could not be found among the gut contents of sampled during the pre- and post-monsoon season, respectively. Among the piscine diets of (23.5%) and (23.5%) were the major prey taxa during pre-monsoon season. The hermit crabs forms the major constituents of both pre- and post-monsoon seasons, among invertebrate taxa. Polychaete, (25.92%) was abundantly consumed invertebrates next to hermit crabs. We noticed that in pre-monsoon was more piscivorous than post-monsoon. As revealed through Kimura-2 parametric pair­wise distance analysis, the diet diversity was relatively higher in post-monsoon. The accumulation curve estimated 57 haplotypes within 14 barcoded species (including the host . Majority of haplotypes were found among fishes (47.36%) followed by Arthropods (28.07%), Annelids (14.03%) and Mollusca (10.52%), respectively. This study also highlights that there is a growing concern about aggressive predation on commercially important stocks of fish and invertebrates. We will continue to expand the coverage of species barcoded in the reference database, which will become more significant as meta- and environmental DNA barcoding techniques become cheaper and prevalent.