Optical manipulation of the charge-density-wave state in RbV3Sb5.

Broken time-reversal symmetry in the absence of spin order indicates the presence of unusual phases such as orbital magnetism and loop currents1-4. The recently discovered kagome superconductors AV3Sb5 (where A is K, Rb or Cs)5,6 display an exotic charge-density-wave (CDW) state and have emerged as a strong candidate for materials hosting a loop current phase. The idea that the CDW breaks time-reversal symmetry7-14 is, however, being intensely debated due to conflicting experimental data15-17. Here we use laser-coupled scanning tunnelling microscopy to study RbV3Sb5. By applying linearly polarized light along high-symmetry directions, we show that the relative intensities of the CDW peaks can be reversibly switched, implying a substantial electro-striction response, indicative of strong nonlinear electron-phonon coupling. A similar CDW intensity switching is observed with perpendicular magnetic fields, which implies an unusual piezo-magnetic response that, in turn, requires time-reversal symmetry breaking. We show that the simplest CDW that satisfies these constraints is an out-of-phase combination of bond charge order and loop currents that we dub a congruent CDW flux phase. Our laser scanning tunnelling microscopy data open the door to the possibility of dynamic optical control of complex quantum phenomenon in correlated materials.

Direct observation of the collective modes of the charge density wave in the kagome metal CsV3Sb5.

A recently discovered group of kagome metals AV[Formula: see text]Sb[Formula: see text] (A = K, Rb, Cs) exhibit a variety of intertwined unconventional electronic phases, which emerge from a puzzling charge density wave phase. Understanding of this charge-ordered parent phase is crucial for deciphering the entire phase diagram. However, the mechanism of the charge density wave is still controversial, and its primary source of fluctuations-the collective modes-has not been experimentally observed. Here, we use ultrashort laser pulses to melt the charge order in CsV[Formula: see text]Sb[Formula: see text] and record the resulting dynamics using femtosecond angle-resolved photoemission. We resolve the melting time of the charge order and directly observe its amplitude mode, imposing a fundamental limit for the fastest possible lattice rearrangement time. These observations together with ab initio calculations provide clear evidence for a structural rather than electronic mechanism of the charge density wave. Our findings pave the way for a better understanding of the unconventional phases hosted on the kagome lattice.

Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing.

BACKGROUND: SARS-CoV-2 genomic analysis has been key to the provision of valuable data to meet both epidemiological and clinical demands. High-throughput sequencing, generally Illumina-based, has been necessary to ensure the widest coverage in global variant tracking. However, a speedier response is needed for nosocomial outbreak analyses and rapid identification of patients infected by emerging VOCs. An alternative based on nanopore sequencing may be better suited to delivering a faster response when required; however, although there are several studies offering side-by-side comparisons of Illumina and nanopore sequencing, evaluations of the usefulness in the hospital routine of the faster availability of data provided by nanopore are still lacking. RESULTS: We performed a prospective 10-week nanopore-based sequencing in MinION in a routine laboratory setting, including 83 specimens where a faster response time was necessary. The specimens analyzed corresponded to i) international travellers in which lineages were assigned to determine the proper management/special isolation of the patients; ii) nosocomial infections and health-care-worker infections, where SNP-based comparisons were required to rule in/out epidemiological relationships and tailor specific interventions iii) sentinel cases and breakthrough infections to timely report to the Public Health authorities. MinION-based sequencing was compared with the standard procedures, supported on Illumina sequencing; MinION accelerated the delivery of results (anticipating results 1-12 days) and reduced costs per sample by 28€ compared to Illumina, without reducing accuracy in SNP calling. CONCLUSIONS: Parallel integration of Illumina and nanopore sequencing strategies is a suitable solution to ensure both high-throughput and rapid response to cope with accelerating the surveillance demands of SARS-CoV-2 while also maintaining accuracy.

A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.

BACKGROUND: During the pandemic, whole genome sequencing was critical to characterize SARS-CoV-2 for surveillance, clinical and therapeutical purposes. However, low viral loads in specimens often led to suboptimal sequencing, making lineage assignment and phylogenetic analysis difficult. We propose an alternative approach to sequencing these specimens that involves sequencing in triplicate and concatenation of the reads obtained using bioinformatics. This proposal is based on the hypothesis that the uncovered regions in each replicate differ and that concatenation would compensate for these gaps and recover a larger percentage of the sequenced genome. RESULTS: Whole genome sequencing was performed in triplicate on 30 samples with Ct > 32 and the benefit of replicate read concatenation was assessed. After concatenation: i) 28% of samples reached the standard quality coverage threshold (> 90% genome covered > 30x); ii) 39% of samples did not reach the coverage quality thresholds but coverage improved by more than 40%; and iii) SARS-CoV-2 lineage assignment was possible in 68.7% of samples where it had been impaired. CONCLUSIONS: Concatenation of reads from replicate sequencing reactions provides a simple way to access hidden information in the large proportion of SARS-CoV-2-positive specimens eliminated from analysis in standard sequencing schemes. This approach will enhance our potential to rule out involvement in outbreaks, to characterize reinfections and to identify lineages of concern for surveillance or therapeutical purposes.

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain.

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.

Frequent Emergence of Resistance Mutations Following Complex Intra-Host Genomic Dynamics in SARS-CoV-2 Patients Receiving Sotrovimab.

The emergence of the Omicron variant of SARS-CoV-2 represented a challenge to the treatment of COVID-19 using monoclonal antibodies. Only Sotrovimab maintained partial activity, allowing it to be used in high-risk patients infected with the Omicron variant. However, reports of resistance mutations to Sotrovimab demand efforts to better understand the intra-patient emergence of Sotrovimab resistance. A retrospective genomic analysis was conducted on respiratory samples from immunocompromised patients infected with SARS-CoV-2 who received Sotrovimab at our hospital between December 2021 and August 2022. The study involved 95 sequential specimens from 22 patients (1 to 12 samples/patient; 3 to 107 days post-infusion; threshold cycle [CT] ≤ 32). Resistance mutations (in P337, E340, K356, and R346) were detected in 68% of cases; the shortest time to detection of a resistance mutation was 5 days after Sotrovimab infusion. The dynamics of resistance acquisition were highly complex, with up to 11 distinct amino acid changes in specimens from the same patient. In two patients, the mutation distribution was compartmentalized in respiratory samples from different sources. This is the first study to examine the acquisition of Sotrovimab resistance in the BA.5 lineage, enabling us to determine the lack of genomic or clinical differences between Sotrovimab resistance in BA.5 relative to that in BA.1/2. Across all Omicron lineages, the acquisition of resistance delayed SARS-CoV-2 clearance (40.67 versus 19.5 days). Close, real-time genomic surveillance of patients receiving Sotrovimab should be mandatory to facilitate early therapeutic interventions.

Kernel weight contribution to yield genetic gain of maize: a global review and US case studies.

Over the past century of maize (Zea mays L.) breeding, grain yield progress has been the result of improvements in several other intrinsic physiological and morphological traits. In this study, we describe (i) the contribution of kernel weight (KW) to yield genetic gain across multiple agronomic settings and breeding programs, and (ii) the physiological bases for improvements in KW for US hybrids. A global-scale literature review concludes that rates of KW improvement in US hybrids were similar to those of other commercial breeding programs but extended over a longer period of time. There is room for a continued increase of kernel size in maize for most of the genetic materials analysed, but the trade-off between kernel number and KW poses a challenge for future yield progress. Through phenotypic characterization of Pioneer Hi-Bred ERA hybrids in the USA, we determine that improvements in KW have been predominantly related to an extended kernel-filling duration. Likewise, crop improvement has conferred on modern hybrids greater KW plasticity, expressed as a better ability to respond to changes in assimilate availability. Our analysis of past trends and current state of development helps to identify candidate targets for future improvements in maize.

Reproductive resilience but not root architecture underpins yield improvement under drought in maize.

Because plants capture water and nutrients through roots, it was proposed that changes in root systems architecture (RSA) might underpin the 3-fold increase in maize (Zea mays L.) grain yield over the last century. Here we show that both RSA and yield have changed with decades of maize breeding, but not the crop water uptake. Results from X-ray phenotyping in controlled environments showed that single cross (SX) hybrids have smaller root systems than double cross (DX) hybrids for root diameters between 2465 µm and 181µm (P<0.05). Soil water extraction measured under field conditions ranged between 2.6 mm d-1 and 2.9 mm d-1 but were not significantly different between SX and DX hybrids. Yield and yield components were higher for SX than DX hybrids across densities and irrigation (P<0.001). Taken together, the results suggest that changes in RSA were not the cause of increased water uptake but an adaptation to high-density stands used in modern agriculture. This adaptation may have contributed to shift in resource allocation to the ear and indirectly improved reproductive resilience. Advances in root physiology and phenotyping can create opportunities to maintain long-term genetic gain in maize, but a shift from ideotype to crop and production system thinking will be required.

Vaccination in rheumatic disease patients: results of a pilot quality improvement program.

OBJECTIVES: Patients with rheumatic diseases (RD) are at increased risk of infections. Vaccination is recognized as a successful public health measure and is recommended for RD patients. The aim of this study was to describe the strategies implemented in an academic rheumatology outpatient clinic as part of a fellow-in-training-led vaccination quality improvement (QI) program and to explore the vaccination uptake before and one year after the implementation. MATERIAL AND METHODS: The program's objective is the promotion of vaccination among patients and rheumatology fellows (by educational interventions, development of vaccination charts and orders, and modifications to electronic medical records to register vaccination dates and generate reminders). As part of the continuous evaluation of the QI program, a descriptive cross-sectional study was performed to evaluate vaccine uptake pre- and post-interventions and vaccination barriers one year after implementation. Consecutive patients with RD answered a self-administered questionnaire. Results are shown as descriptive statistics. RESULTS: Before the program started 73 patients were surveyed and 102 patients one year after. The vaccination uptake rates for influenza pre- and post-interventions were 43% and 55%; for pneumococcal vaccination they were 26% and 30%; for herpes zoster they were 0% and 4%; for human papillomavirus they were 4% and 10%; for hepatitis B (HBV) they were 19% and 25% respectively. Eighty percent of patients reported some barriers to receiving any of the previous vaccines. The three main reasons for not receiving a vaccine were the lack of recommendation, the lack of availability, and the belief that vaccines do not work. CONCLUSIONS: The implementation of a pilot vaccination QI program led by rheumatology fellows-in-training showed promising preliminary benefits in the vaccination uptake among RD patients and helps to evaluate the barriers to surpass.

Correction to: A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone.

The original article [1] contains three erroneous mentions of usage of a restriction enzyme-BstZ17I-in the Methods section as displayed in the following sentences.

Severe Respiratory Illness Outbreak Associated with Human Coronavirus NL63 in a Long-Term Care Facility.

We describe an outbreak of severe respiratory illness associated with human coronavirus NL63 in a long-term care facility in Louisiana in November 2017. Six of 20 case-patients were hospitalized with pneumonia, and 3 of 20 died. Clinicians should consider human coronavirus NL63 for patients in similar settings with respiratory disease.

A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone.

BACKGROUND: Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employed as genome editing tools in wide ranging organisms. Here, we provide a detailed protocol to truncate genes in mammalian cells using CRISPR Cas9 editing. We describe custom donor vector construction using Gibson assembly with the commonly utilized pcDNA3 vector as the backbone. RESULTS: We describe a step-by-step method to truncate genes of interest in mammalian cell lines using custom-made donor vectors. Our method employs 2 guide RNAs, mutant Cas9D10A nickase (Cas9 = CRISPR associated sequence 9), and a custom-made donor vector for homologous recombination to precisely truncate a gene of interest with a selectable neomycin resistance cassette (NPTII: Neomycin Phosphotransferase II). We provide a detailed protocol on how to design and construct a custom donor vector using Gibson assembly (and the commonly utilized pcDNA3 vector as the backbone) allowing researchers to obtain specific gene modifications of interest (gene truncation, gene deletion, epitope tagging or knock-in mutation). Selection of mutants in mammalian cell lines with G418 (Geneticin) combined with several screening methods: western blot analysis, polymerase chain reaction, and Sanger sequencing resulted in streamlined mutant isolation. Proof of principle experiments were done in several mammalian cell lines. CONCLUSIONS: Here we describe a detailed protocol to employ CRISPR Cas9 genome editing to truncate genes of interest using the commonly employed expression vector pcDNA3 as the backbone for the donor vector. Providing a detailed protocol for custom donor vector design and construction will enable researchers to develop unique genome editing tools. To date, detailed protocols for CRISPR Cas9 custom donor vector construction are limited (Lee et al. in Sci Rep 5:8572, 2015; Ma et al. in Sci Rep 4:4489, 2014). Custom donor vectors are commercially available, but can be expensive. Our goal is to share this protocol to aid researchers in performing genetic investigations that require custom donor vectors for specialized applications (specific gene truncations, knock-in mutations, and epitope tagging applications).

Evaluation of Mpox Exposures and Outcomes in Workplaces, 6 Jurisdictions, June 1-August 31, 2022.

OBJECTIVES: The risk for mpox virus (MPXV) transmission in most workplaces has not been thoroughly assessed in the context of the 2022 global mpox outbreak. Our objectives were to describe mpox case patients who worked while infectious and the subsequent workplace contact tracing efforts, risk assessments, and outcomes. METHODS: The Centers for Disease Control and Prevention requested information from health departments in the United States in September 2022 to identify people with confirmed or probable mpox who worked outside the home while infectious, either before or after diagnosis, from June 1 through August 31, 2022. We collected and summarized data on demographic, clinical, and workplace characteristics of case patients and workplace contact investigations. We stratified data by industry and occupation categories. RESULTS: In total, 102 case patients were reported by 6 jurisdictions. The most common industries were accommodation and food services (19.8%) and professional business, management, and technical services (17.0%). Contact investigations identified 178 total contacts; 54 cases (52.9%) had no contacts identified. Of 178 contacts, 54 (30.3%) were recommended to receive postexposure prophylaxis (PEP) and 18 (10.1%) received PEP. None of the contacts developed a rash or were tested for orthopox or mpox, and none were reported to have confirmed or probable mpox. CONCLUSION: Data from 6 jurisdictions suggest that the risk of MPXV transmission from workers to others in workplace settings in many industries is low. These findings might support future updates to exposure risk classifications and work activity recommendations for patients. These findings also demonstrate the importance of collecting and analyzing occupation and industry data in case reports to better understand risks in workplaces.

Advances in high-pressure laser floating zone growth: The Laser Optical Kristallmacher II (LOKII).

The optical floating zone crystal growth technique is a well-established method for obtaining large, high-purity single crystals. While the floating zone method has been constantly evolving for over six decades, the development of high-pressure (up to 1000 bar) growth systems has only recently been realized via the combination of laser-based heating sources with an all-metal chamber. While our inaugural high-pressure laser floating zone furnace design demonstrated the successful growth of new volatile and metastable phases, the furnace design faces several limitations with imaging quality, heating profile control, and chamber cooling power. Here, we present a second-generation design of the high-pressure laser floating zone furnace, "Laser Optical Kristallmacher II" (LOKII), and demonstrate that this redesign facilitates new advances in crystal growth by highlighting several exemplar materials: α-Fe2O3, ß-Ga2O3, and La2CuO4+δ. Notably, for La2CuO4+δ, we demonstrate the feasibility and long-term stability of traveling solvent floating zone growth under a record pressure of 700 bar.

Microevolution, reinfection and highly complex genomic diversity in patients with sequential isolates of Mycobacterium abscessus.

Mycobacterium abscessus is an opportunistic, extensively drug-resistant non-tuberculous mycobacterium. Few genomic studies consider its diversity in persistent infections. Our aim was to characterize microevolution/reinfection events in persistent infections. Fifty-three sequential isolates from 14 patients were sequenced to determine SNV-based distances, assign resistance mutations and characterize plasmids. Genomic analysis revealed 12 persistent cases (0-13 differential SNVs), one reinfection (15,956 SNVs) and one very complex case (23 sequential isolates over 192 months), in which a first period of persistence (58 months) involving the same genotype 1 was followed by identification of a genotype 2 (76 SNVs) in 6 additional alternating isolates; additionally, ten transient genotypes (88-243 SNVs) were found. A macrolide resistance mutation was identified from the second isolate. Despite high diversity, the genotypes shared a common phylogenetic ancestor and some coexisted in the same specimens. Genomic analysis is required to access the true intra-patient complexity behind persistent infections involving M. abscessus.

Taxonomic reassessment of Tetrapygus niger (Arbacioida, Echinoidea): molecular and morphological evidence support its placement in Arbacia.

The echinoid genus Tetrapygus was initially described by L. Agassiz (1841) based on a single species, Tetrapygus niger Molina, 1782. Since the extensive work conducted by Mortensen (1935), Tetrapygus has received limited taxonomic attention over the past century. Recent discoveries of new fossil species of Arbacia Gray, 1835 from the upper Pliocene of northern Chile revealed striking morphological similarities between the two distinct Arbaciidae genera Arbacia and Tetrapygus. These findings compelled new investigations to evaluate the taxonomic status of these genera. Based on molecular mitochondrial (COI), nuclear (28S), and morphological evidence, Tetrapygus niger is here recovered as the sister species to Arbacia dufresnii, both species forming a clade within the phylogeny of South American species of Arbacia. Consequently, the diagnosis and description of Tetrapygus niger are here revised, and the species is reattributed to Arbacia, as previously proposed by A. Agassiz in Agassiz & Desor (1846) under the species name Arbacia nigra. An emended diagnosis of Arbacia is also proposed in light of these new findings.