Effect of Trastuzumab–HER2 Complex Formation on Stress-Induced Modifications in the CDRs of Trastuzumab

Asparagine deamidation and aspartic acid isomerization in the complementarity determining regions (CDRs) of monoclonal antibodies may alter their affinity to the target antigen. Trastuzumab has two hot spots for deamidation and one position for isomerization in the CDRs. Little is known how complex formation with its target antigen HER2 affects these modifications. Modifications in the CDRs of trastuzumab were thus compared between the free antibody and the trastuzumab–HER2 complex when stressed under physiological conditions at 37°C. Complex formation and stability of the complex upon stressing were assessed by size-exclusion chromatography. Deamidation of light-chain Asn-30 (Lc-Asn-30) was extensive when trastuzumab was stressed free but reduced about 10-fold when the antibody was stressed in complex with HER2. Almost no deamidation of heavy-chain (Hc-Asn-55) was detected in the trastuzumab–HER2 complex, while deamidation was observed when the antibody was stressed alone. Hc-Asp-102 isomerization, a modification that critically affects biological activity, was observed to a moderate degree when the free antibody was stressed but was not detected at all in the trastuzumab–HER2 complex. This shows that complex formation has a major influence on critical modifications in the CDRs of trastuzumab.

Hydrothermal Activities on C-Complex Asteroids Induced by Radioactivity

C-complex asteroids, rich in carbonaceous materials, are potential sources of Earth’s volatile inventories. They are spectrally dark resembling primitive carbonaceous meteorites, and thus, C-complex asteroids are thought to be potential parent bodies of carbonaceous meteorites. However, the substantial number of C-complex asteroids exhibits surface spectra with weaker hydroxyl absorption than water-rich carbonaceous meteorites. Rather, they best correspond to meteorites showing evidence for dehydration, commonly attributed to impact heating. Here, we report an old radiometric age of 4564.7 million years ago for Ca carbonates from the Jbilet Winselwan meteorite analogous to dehydrated C-complex asteroids. The carbonates are enclosed by a high-temperature polymorph of Ca sulfates, suggesting thermal metamorphism at >300°C subsequently after aqueous alteration. This old age indicates the early onset of aqueous alteration and subsequent thermal metamorphism driven by the decay of short-lived radionuclides rather than impact heating. The breakup of original asteroids internally heated by radioactivity should result in asteroid families predominantly consisting of thermally metamorphosed materials. This explains the common occurrence of dehydrated C-complex asteroids.

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.

The APC/CFZY–1/Cdc20 Complex Coordinates With OMA-1 to Regulate the Oocyte-to-Embryo Transition in Caenorhabditis elegans

During oocyte maturation and the oocyte-to-embryo transition, key developmental regulators such as RNA-binding proteins coordinate translation of particular messenger RNA (mRNAs) and related developmental processes by binding to their cognate maternal mRNAs. In the nematode Caenorhabditis elegans, these processes are regulated by a set of CCCH zinc finger proteins. Oocyte maturation defective-1 (OMA-1) and OMA-2 are two functionally redundant CCCH zinc finger proteins that turnover rapidly during the first embryonic cell division. These turnovers are required for proper transition from oogenesis to embryogenesis. A gain-of-function mutant of OMA-1, oma-1(zu405), stabilizes and delays degradation of OMA-1, resulting in delayed turnover and mis-segregation of other cell fate determinants, which eventually causes embryonic lethality. We performed a large-scale forward genetic screen to identify suppressors of the oma-1(zu405) mutant. We show here that multiple alleles affecting functions of various anaphase promoting complex/cyclosome (APC/C) subunits, including MAT-1, MAT-2, MAT-3, EMB-30, and FZY-1, suppress the gain-of-function mutant of OMA-1. Transcriptome analysis suggested that overall transcription in early embryos occurred after introducing mutations in APC/C genes into the oma-1(zu405) mutant. Mutations in APC/C genes prevent OMA-1 enrichment in P granules and correct delayed degradation of downstream cell fate determinants including pharynx and intestine in excess-1 (PIE-1), posterior segregation-1 (POS-1), muscle excess-3 (MEX-3), and maternal effect germ-cell defective-1 (MEG-1). We demonstrated that only the activator FZY-1, but not FZR-1, is incorporated in the APC/C complex to regulate the oocyte-to-embryo transition. Our findings suggested a genetic relationship linking the APC/C complex and OMA-1, and support a model in which the APC/C complex promotes P granule accumulation and modifies RNA binding of OMA-1 to regulate the oocyte-to-embryo transition process.

VLT/SPHERE imaging survey of the largest main-belt asteroids: Final results and synthesis

Context. Until recently, the 3D shape, and therefore density (when combining the volume estimate with available mass estimates), and surface topography of the vast majority of the largest (D ≥ 100 km) main-belt asteroids have remained poorly constrained. The improved capabilities of the SPHERE/ZIMPOL instrument have opened new doors into ground-based asteroid exploration. Aims. To constrain the formation and evolution of a representative sample of large asteroids, we conducted a high-angular-resolution imaging survey of 42 large main-belt asteroids with VLT/SPHERE/ZIMPOL. Our asteroid sample comprises 39 bodies with D ≥ 100 km and in particular most D ≥ 200 km main-belt asteroids (20/23). Furthermore, it nicely reflects the compositional diversity present in the main belt as the sampled bodies belong to the following taxonomic classes: A, B, C, Ch/Cgh, E/M/X, K, P/T, S, and V. Methods. The SPHERE/ZIMPOL images were first used to reconstruct the 3D shape of all targets with both the ADAM and MPCD reconstruction methods. We subsequently performed a detailed shape analysis and constrained the density of each target using available mass estimates including our own mass estimates in the case of multiple systems. Results. The analysis of the reconstructed shapes allowed us to identify two families of objects as a function of their diameters, namely “spherical” and “elongated” bodies. A difference in rotation period appears to be the main origin of this bimodality. In addition, all but one object (216 Kleopatra) are located along the Maclaurin sequence with large volatile-rich bodies being the closest to the latter. Our results further reveal that the primaries of most multiple systems possess a rotation period of shorter than 6 h and an elongated shape (c∕a ≤ 0.65). Densities in our sample range from ~1.3 g cm−3 (87 Sylvia) to ~4.3 g cm−3 (22 Kalliope). Furthermore, the density distribution appears to be strongly bimodal with volatile-poor (ρ ≥ 2.7 g cm−3) and volatile-rich (ρ ≤ 2.2 g cm−3) bodies. Finally, our survey along with previous observations provides evidence in support of the possibility that some C-complex bodies could be intrinsically related to IDP-like P- and D-type asteroids, representing different layers of a same body (C: core; P/D: outer shell). We therefore propose that P/ D-types and some C-types may have the same origin in the primordial trans-Neptunian disk.

The N-Terminal Region of the Polo Kinase Cdc5 is Required for Downregulation of the Meiotic Recombination Checkpoint

During meiosis, the budding yeast polo-like kinase Cdc5 is a crucial driver of the prophase I to meiosis I (G2/M) transition. The meiotic recombination checkpoint restrains cell cycle progression in response to defective recombination to ensure proper distribution of intact chromosomes to the gametes. This checkpoint detects unrepaired DSBs and initiates a signaling cascade that ultimately inhibits Ndt80, a transcription factor required for CDC5 gene expression. Previous work revealed that overexpression of CDC5 partially alleviates the checkpoint-imposed meiotic delay in the synaptonemal complex-defective zip1Δ mutant. Here, we show that overproduction of a Cdc5 version (Cdc5-ΔN70), lacking the N-terminal region required for targeted degradation of the protein by the APC/C complex, fails to relieve the zip1Δ-induced meiotic delay, despite being more stable and reaching increased protein levels. However, precise mutation of the consensus motifs for APC/C recognition (D-boxes and KEN) has no effect on Cdc5 stability or function during meiosis. Compared to the zip1Δ single mutant, the zip1Δ cdc5-ΔN70 double mutant exhibits an exacerbated meiotic block and reduced levels of Ndt80 consistent with persistent checkpoint activity. Finally, using a CDC5-inducible system, we demonstrate that the N-terminal region of Cdc5 is essential for its checkpoint erasing function. Thus, our results unveil an additional layer of regulation of polo-like kinase function in meiotic cell cycle control.