Mathematics at the eve of a historic transition in biology

A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently, biology is undergoing a historic transition from qualitative, phenomenological and descriptive to quantitative, analytical and predictive. Mathematics, again, becomes a driving force behind this new transition in biology.Comment: 5 pages, 2 figure

An integrative description of a population of Mesobiotus radiatus (Pilato, Binda & Catanzaro, 1991) from Kenya

In a moss sample collected from Mount Kulal in Kenya, a new population of Mesobiotus radiatus was found. Given that the original description of M. radiatus was based solely on the morphology observed by light microscopy and measurements based mostly on a single individual, here we describe the new population by means of integrative taxonomy and a large sample size. We provide an integrative description comprising a comprehensive set of morphometric and morphological data from light and scanning microscopy as well as nucleotide sequences of three nuclear fragments (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial fragment (COI). Mesobiotus radiatus is most similar to M. binieki, M. coronatus, M. patiens, M. perfidus, M. philippinicus, M. pseudocoronatus, M. pseudopatiens, M. rigidus, M. simulans, and M. wuzhishanensis, but differs from them mainly by egg morphology and morphometry, and some characters of adult specimens

Role of (p)ppGpp in Viability and Biofilm Formation of Actinobacillus pleuropneumoniae S8.

Actinobacillus pleuropneumoniae is a Gram-negative bacterium and the cause of porcine pleuropneumonia. When the bacterium encounters nutritional starvation, the relA-dependent (p)ppGpp-mediated stringent response is activated. The modified nucleotides guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and guanosine 5'-triphosphate 3'-diphosphate (pppGpp) are known to be signaling molecules in other prokaryotes. Here, to investigate the role of (p)ppGpp in A. pleuropneumoniae, we created a mutant A. pleuropneumoniae strain, S8ΔrelA, which lacks the (p)ppGpp-synthesizing enzyme RelA, and investigated its phenotype in vitro. S8ΔrelA did not survive after stationary phase (starvation condition) and grew exclusively as non-extended cells. Compared to the wild-type (WT) strain, the S8ΔrelA mutant had an increased ability to form a biofilm. Transcriptional profiles of early stationary phase cultures revealed that a total of 405 bacterial genes were differentially expressed (including 380 up-regulated and 25 down-regulated genes) in S8ΔrelA as compared with the WT strain. Most of the up-regulated genes are involved in ribosomal structure and biogenesis, amino acid transport and metabolism, translation cell wall/membrane/envelope biogenesis. The data indicate that (p)ppGpp coordinates the growth, viability, morphology, biofilm formation and metabolic ability of A. pleuropneumoniae in starvation conditions. Furthermore, S8ΔrelA could not use certain sugars nor produce urease which has been associated with the virulence of A. pleuropneumoniae, suggesting that (p)ppGpp may directly or indirectly affect the pathogenesis of A. pleuropneumoniae during the infection process. In summary, (p)ppGpp signaling represents an essential component of the regulatory network governing stress adaptation and virulence in A. pleuropneumoniae

Role of fetal MRI in the evaluation of isolated and non-isolated corpus callosum dysgenesis: results of a cross-sectional study

PURPOSE: The aims of this study were to characterize isolated and non-isolated forms of corpus callosum dysgenesis (CCD) at fetal magnetic resonance imaging (MRI) and to identify early predictors of associated anomalies. METHODS: We retrospectively analyzed 104 fetuses with CCD undergoing MRI between 2006 and 2016. Corpus callosum, cavum septi pellucidi, biometry, presence of ventriculomegaly, gyration anomalies, cranio-encephalic abnormalities and body malformations were evaluated. Results of genetic tests were also recorded. RESULTS: At MRI, isolated CCD was 26.9%, the rest being associated to other abnormalities. In the isolated group, median gestational age at MRI was lower in complete agenesis than in hypoplasia (22 vs 28 weeks). In the group with additional findings, cortical dysplasia was the most frequently associated feature (P = 0.008), with a more frequent occurrence in complete agenesis (70%) versus other forms; mesial frontal lobes were more often involved than other cortical regions (P = 0.006), with polymicrogyria as the most frequent cortical malformation (40%). Multivariate analysis confirmed the association between complete agenesis and cortical dysplasia (odds ratio = 7.29, 95% confidence interval 1.51-35.21). CONCLUSIONS: CCD is often complicated by other intra-cranial and extra-cranial findings (cortical dysplasias as the most prevalent) that significantly affect the postnatal prognosis. The present study showed CCD with associated anomalies as more frequent than isolated (73.1%). In isolated forms, severe ventriculomegaly was a reliable herald of future appearance of associated features

Alternatívy k MILP pre rozvrhovanie dávkových banských procesov

Cie¾om príspevku je navrhnú monos, nahradenia optimalizaèných metód na báze zmieaného celoèíselného programovania pouitím pribliných metód rozhodovania (heuristika) v oblasti plánovania a riadenia banských procesov. Výsledkom tohto poèítaèom podporaovaného plánovania sú detailné výrobné rozvrhy vytvorené pod¾a poiadaviek ako sú vysoká efektivita výroby, alebo zníená redukcia odpadov. Tieto problémy patria medzi zloité, NP-úplné problémy, èie ich rieenie je v súèasnosti pod¾a náho názoru pre reálne problémy efektívnejie s pomocou heuristík. Heuristiky uvedené v príspevku sú: simulované íhanie, tabu search a genetické algoritmy. Tabu search(metóda zakázaného preh¾adávania), aj keï sa jedná o heuristiku, je v tandardnej verzii deterministicky stachastická. V prispevku sú zhrnuté hlavné výhody heuristík v porovnaní s MILP, predovetkým ich rýchlos a jednoduchos a teda aj niie nároky na výpoètovú techniku a software, ako aj kvalita poskytovaných výsledkov. Èlánok uvádza struèný popis rieených problémov a základy matematického popisu týchto problémov, zhrnuté sú aj rôzne ciele optimalizácie reprezentované rôznymi cie¾ovými kritériami. Príspevok ïalej popisuje jednotlivé heuristiky, ich princípy, ich vlastnosti a ich monosti, poiadavky ktoré musí úloha splòova, aby bolo moné algoritmus poui. Prekadú z uvedených heuristík uvádzame aj slovný popis jednotlivých èastí algoritmu. Èlánok uvádza jednotlivé výsledky porovnania výkonov týchto heuristík oproti MILP, uvedené sú aj výsledky aplikácie týchto algoritmov na iné podobné problémy v chemickom priemysle. Vzh¾adom k zámerom tohto príspevku text obsahuje aj odkazy na ïaliu literatúru zaoberajúcu sa touto problematikou

The genome incorporated: constructing biodigital identity

The Genome Incorporated examines the proliferation of human genomics across contemporary media cultures. It explores questions about what it means for a technoscience to thoroughly saturate everyday life, and places the interrogation of the science/media relationship at the heart of this enquiry. The book develops a number of case studies in the mediation and consumption of genomics, including: the emergence of new direct-to-the-consumer bioinformatics companies; the mundane propagation of testing and genetic information through lifestyle television programming; and public and private engagements with art and science institutions and events. Through these novel sites, this book examines the proliferating circuits of production and consumption of genetic information and theorizes this as a process of incorporation. Its wide-ranging case studies ensure its appeal to readers across the social sciences

Current commercialization status of electrowetting-on-dielectric (EWOD) digital microfluidics.

The emergence of electrowetting-on-dielectric (EWOD) in the early 2000s made the once-obscure electrowetting phenomenon practical and led to numerous activities over the last two decades. As an eloquent microscale liquid handling technology that gave birth to digital microfluidics, EWOD has served as the basis for many commercial products over two major application areas: optical, such as liquid lenses and reflective displays, and biomedical, such as DNA library preparation and molecular diagnostics. A number of research or start-up companies (e.g., Phillips Research, Varioptic, Liquavista, and Advanced Liquid Logic) led the early commercialization efforts and eventually attracted major companies from various industry sectors (e.g., Corning, Amazon, and Illumina). Although not all of the pioneering products became an instant success, the persistent growth of liquid lenses and the recent FDA approvals of biomedical analyzers proved that EWOD is a powerful tool that deserves a wider recognition and more aggressive exploration. This review presents the history around major EWOD products that hit the market to show their winding paths to commercialization and summarizes the current state of product development to peek into the future. In providing the readers with a big picture of commercializing EWOD and digital microfluidics technology, our goal is to inspire further research exploration and new entrepreneurial adventures

The last common bilaterian ancestor

Many regulatory genes appear to be utilized in at least superficially similar ways in the development of particular body parts in Drosophila and in chordates. These similarities have been widely interpreted as functional homologies, producing the conventional view of the last common protostome-deuterostome ancestor (PDA) as a complex organism that possessed some of the same body parts as modern bilaterians. Here we discuss an alternative view, in which the last common PDA had a less complex body plan than is frequently conceived. This reconstruction alters expectations for Neoproterozoic fossil remains that could illustrate the pathways of bilaterian evolution

Cultivating the macroalgal holobiont: effects of integrated multi-trophic aquaculture on the microbiome of Ulva rigida (chlorophyta)

Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi-Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to their high productivity and environmental sustainability. Complex host-microbiome interactions play a decisive role in macroalgal development, especially in Ulva spp. due to algal growth- and morphogenesis-promoting factors released by associated bacteria. However, our current understanding of the microbial community assembly and structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) to explore the dynamics of beneficial microbes to algal growth and development under IMTA settings, and (iii) to improve current knowledge of host-microbiome interactions. We examined the diversity and taxonomic composition of the prokaryotic communities associated with wild versus IMTA-grown Ulva rigida and surrounding seawater by using 16S rRNA gene amplicon sequencing. With 3141 Amplicon Sequence Variants (ASVs), the prokaryotic richness was, overall, higher in water than in association with U. rigida. Bacterial ASVs were more abundant in aquaculture water samples than water collected from the lagoon. The beta diversity analysis revealed distinct prokaryotic communities associated with Ulva collected in both aquacultures and coastal waters. Aquaculture samples (water and algae) shared 22% of ASVs, whereas natural, coastal lagoon samples only 9%. While cultivated Ulva selected 239 (8%) host-specific ASVs, wild specimens possessed more than twice host-specific ASVs (17%). Cultivated U. rigida specimens enriched the phyla Cyanobacteria, Planctomycetes, Verrucomicrobia, and Proteobacteria. Within the Gammaproteobacteria, while Glaciecola mostly dominated the microbiome in cultivated algae, the genus Granulosicoccus characterized both Ulva microbiomes. In both wild and IMTA settings, the phylum Bacteroidetes was more abundant in the bacterioplankton than in direct association with U. rigida. However, we observed that the Saprospiraceae family within this phylum was barely present in lagoon water but very abundant in aquaculture water. Aquaculture promoted the presence of known morphogenesis-inducing bacteria in water samples. Our study suggests that IMTA significantly shaped the structure and composition of the microbial community of the rearing water and cultivated U. rigida. Detailed analysis revealed the presence of previously undetected taxa associated with Ulva, possessing potentially unknown functional traits.European Union (EU)642575; German Research Foundation (DFG) CRC 1127 ChemBioSys;COST Action "Phycomorph" FA1406info:eu-repo/semantics/publishedVersio