Protein-mediated nanoscale biotemplating

Biomimetics--the concept of taking ideas from nature and implementing them in technology--has found particular use for the development of nanoscale materials. One such approach employs protein-mediated biotemplating for the nanostructuring of inorganic material. Recently, two key advances have been witnessed in this field. Firstly, the number of successfully employed biotemplates, including feasibility demonstrations of using three-dimensional crystalline structures, has been expanded. Secondly, the introduction of site-directed mutations on the protein template, or the display of peptides that exhibit effective biorecognition sequences for inorganic structures, has led to substantial improvements in our ability to control protein-mediated biotemplating. Taken together, these achievements will pave the way for the successful application of protein-mediated biotemplating in the future.     

The nuts and bolts of germ-cell migration

In many species, primordial germ cells (PGCs) migrate from the position where they are specified to the site where the gonad develops, where they differentiate into sperm and egg. Germ cells thus serve as an excellent model for studying cell migration in the context of the live organism. In recent years, a number of cues directing the migration of the cells towards their target were identified and some of the relevant molecules and biochemical pathways were revealed. In this review we present those results, focusing on 'cell mechanics' of the process including cell adhesion, traction generation and cell polarization.     

The quadruplex r(CGG)n destabilizing cationic porphyrin TMPyP4 cooperates with hnRNPs to increase the translation efficiency of fragile X premutation mRNA

The 5′ untranslated region of the FMR1 gene which normally includes 4–55 d(CGG) repeats expands to > 55–200 repeats in carriers of fragile X syndrome premutation. Although the levels of premutation FMR1 mRNA in carrier cells are 5–10-fold higher than normal, the amount of the product FMR protein is unchanged or reduced. We demonstrated previously that premutation r(CGG)_n tracts formed quadruplex structures that impeded translation and lowered the efficiency of protein synthesis. Normal translation could be restored in vivo by the quadruplex r(CGG)_n destabilizing action of CBF-A and hnRNP A2 proteins. Here we report that the quadruplex-interacting cationic porphyrin TMPyP4 by itself and in cooperation with CBF-A or hnRNP A2 also unfolded quadruplex r(CGG)_n and increased the efficiency of translation of 5′-(CGG)₉₉ containing reporter firefly (FL) mRNA. TMPyP4 destabilized in vitro a (CGG)₃₃ intramolecular quadruplex structure and enhanced the translation of 5′-(CGG)₉₉-FL mRNA in a rabbit reticulocyte lysate and in HEK293 cells. The efficiency of translation of (CGG)₉₉-FL mRNA was additively increased in cells exposed to TMPyP4 together with CBF-A. Whereas low doses of TMPyP4, CBF-A or hnRNP A2 by themselves did not affect the in vivo utilization of (CGG)₉₉-FL mRNA, introduction of TMPyP4 together with either protein synergistically augmented its translation efficiency.     

Modular architecture of Munc13/calmodulin complexes: dual regulation by Ca2+ and possible function in short‐term synaptic plasticity

Ca²⁺ signalling in neurons through calmodulin (CaM) has a prominent function in regulating synaptic vesicle trafficking, transport, and fusion. Importantly, Ca²⁺–CaM binds a conserved region in the priming proteins Munc13‐1 and ubMunc13‐2 and thus regulates synaptic neurotransmitter release in neurons in response to residual Ca²⁺ signals. We solved the structure of Ca²⁺₄–CaM in complex with the CaM‐binding domain of Munc13‐1, which features a novel 1‐5‐8‐26 CaM‐binding motif with two separated mobile structural modules, each involving a CaM domain. Photoaffinity labelling data reveal the same modular architecture in the complex with the ubMunc13‐2 isoform. The N‐module can be dissociated with EGTA to form the half‐loaded Munc13/Ca²⁺₂–CaM complex. The Ca²⁺ regulation of these Munc13 isoforms can therefore be explained by the modular nature of the Munc13/Ca²⁺–CaM interactions, where the C‐module provides a high‐affinity interaction activated at nanomolar [Ca²⁺]_i, whereas the N‐module acts as a sensor at micromolar [Ca²⁺]_i. This Ca²⁺/CaM‐binding mode of Munc13 likely constitutes a key molecular correlate of the characteristic Ca²⁺‐dependent modulation of short‐term synaptic plasticity.     

Automated assessment reveals that the extinction risk of reptiles is widely underestimated across space and phylogeny

The Red List of Threatened Species, published by the International Union for Conservation of Nature (IUCN), is a crucial tool for conservation decision-making. However, despite substantial effort, numerous species remain unassessed or have insufficient data available to be assigned a Red List extinction risk category. Moreover, the Red Listing process is subject to various sources of uncertainty and bias. The development of robust automated assessment methods could serve as an efficient and highly useful tool to accelerate the assessment process and offer provisional assessments. Here, we aimed to (1) present a machine learning–based automated extinction risk assessment method that can be used on less known species; (2) offer provisional assessments for all reptiles—the only major tetrapod group without a comprehensive Red List assessment; and (3) evaluate potential effects of human decision biases on the outcome of assessments. We use the method presented here to assess 4,369 reptile species that are currently unassessed or classified as Data Deficient by the IUCN. The models used in our predictions were 90% accurate in classifying species as threatened/nonthreatened, and 84% accurate in predicting specific extinction risk categories. Unassessed and Data Deficient reptiles were considerably more likely to be threatened than assessed species, adding to mounting evidence that these species warrant more conservation attention. The overall proportion of threatened species greatly increased when we included our provisional assessments. Assessor identities strongly affected prediction outcomes, suggesting that assessor effects need to be carefully considered in extinction risk assessments. Regions and taxa we identified as likely to be more threatened should be given increased attention in new assessments and conservation planning. Lastly, the method we present here can be easily implemented to help bridge the assessment gap for other less known taxa.

The Red List of Threatened Species, published by the IUCN, is a crucial tool for conservation decision making, but is subject to various sources of uncertainty and bias. Modelling the threat status of all global reptiles identifies increased threat to many groups of reptiles across many regions of the world, beyond those currently recognized; moreover, it highlights the effects of the IUCN assessment procedure on eventual threat categories.     

Identification of the midgut microbiota of An. stephensi and An. maculipennis for their application as a paratransgenic tool against malaria

The midgut microbiota associated with Anopheles stephensi and Anopheles maculipennis (Diptera: Culicidae) was investigated for development of a paratransgenesis-based approach to control malaria transmission in Eastern Mediterranean Region (EMR). Here, we present the results of a polymerase chain reaction (PCR) and biochemical-based approaches to identify the female adult and larvae mosquitoe microbiota of these two major malaria vectors, originated from South Eastern and North of Iran. Plating the mosquito midgut contents from lab-reared and field-collected Anopheles spp. was used for microbiota isolation. The gram-negative and gram-positive bacterial colonies were identified by Gram staining and specific mediums. Selected colonies were identified by differential biochemical tests and 16S rRNA gene sequence analysis. A number of 10 An. stephensi and 32 An. maculipennis adult mosquitoes and 15 An. stephensi and 7 An. maculipennis larvae were analyzed and 13 sequences of 16S rRNA gene bacterial species were retrieved, that were categorized in 3 classes and 8 families. The majority of the identified bacteria were belonged to the γ-proteobacteria class, including Pseudomonas sp. and Aeromonas sp. and the others were some closely related to those found in other vector mosquitoes, including Pantoea, Acinetobacter, Brevundimonas, Bacillus, Sphingomonas, Lysinibacillus and Rahnella. The 16S rRNA sequences in the current study aligned with the reference strains available in GenBank were used for construction of the phylogenetic tree that revealed the relatedness among the bacteria identified. The presented data strongly encourage further investigations, to verify the potential role of the detected bacteria for the malaria control in Iran and neighboring countries.     

Unique features of transcription termination and initiation at closely spaced tandem human genes

The authors regret having omitted grant attributions in the original publication, and the acknowledgments are herewith updated.“This work was supported by grants to IU from the European Research Council (lncImpact project number 863589), the Abisch‐Frenkel Foundation for the Promotion of Life Sciences, and the Kekst Family Institute for Medical Genetics.”The authors apologize for this oversight and any confusion it may have caused.