The geography of climate and the global patterns of species diversity.

Climate's effect on global biodiversity is typically viewed through the lens of temperature, humidity and resulting ecosystem productivity1-6. However, it is not known whether biodiversity depends solely on these climate conditions, or whether the size and fragmentation of these climates are also crucial. Here we shift the common perspective in global biodiversity studies, transitioning from geographic space to a climate-defined multidimensional space. Our findings suggest that larger and more isolated climate conditions tend to harbour higher diversity and species turnover among terrestrial tetrapods, encompassing more than 30,000 species. By considering both the characteristics of climate itself and its geographic attributes, we can explain almost 90% of the variation in global species richness. Half of the explanatory power (45%) may be attributed either to climate itself or to the geography of climate, suggesting a nuanced interplay between them. Our work evolves the conventional idea that larger climate regions, such as the tropics, host more species primarily because of their size7,8. Instead, we underscore the integral roles of both the geographic extent and degree of isolation of climates. This refined understanding presents a more intricate picture of biodiversity distribution, which can guide our approach to biodiversity conservation in an ever-changing world.

Calcium channel blockers potentiate gemcitabine chemotherapy in pancreatic cancer.

There is currently no effective treatment for pancreatic ductal adenocarcinoma (PDAC). While palliative chemotherapy offers a survival benefit to most patients, nearly all will eventually progress on treatment and long-term survivability remains poor. Given the lack of subsequent line treatment options, in this study, we sought to identify novel strategies to prevent, delay, or overcome resistance to gemcitabine, one of the most widely used medications in PDAC. Using a combination of single-cell RNA sequencing and high-throughput proteomic analysis, we identified a subset of gemcitabine-resistant tumor cells enriched for calcium/calmodulin signaling. Pharmacologic inhibition of calcium-dependent calmodulin activation led to the rapid loss of drug-resistant phenotypes in vitro, which additional single-cell RNA sequencing identified was due to impaired activation of the RAS/ERK signaling pathway. Consistent with these observations, calcium chelation or depletion of calcium in the culture media also impaired ERK activation in gemcitabine-resistant cells, and restored therapeutic responses to gemcitabine in vitro. We observed similar results using calcium channel blockers (CCBs) such as amlodipine, which inhibited prosurvival ERK signaling in vitro and markedly enhanced therapeutic responses to gemcitabine in both orthotopic xenografts and transgenic models of PDAC. Combined, these results offer insight into a potential means of gemcitabine resistance and suggest that select CCBs may provide a clinical benefit to PDAC patients receiving gemcitabine-based chemotherapy.

The Efficiency of p27 Cleavage during In Vitro Respiratory Syncytial Virus (RSV) Infection Is Cell Line and RSV Subtype Dependent.

Respiratory syncytial virus (RSV) fusion protein (F) is highly conserved between subtypes A and B (RSV/A and RSV/B). To become fully active, F precursor undergoes enzymatic cleavage to yield F1 and F2 subunits and releases a 27-amino-acid peptide (p27). Virus-cell fusion occurs when RSV F undergoes a conformational change from pre-F to post-F. Previous data show that p27 is detected on RSV F, but questions remain regarding if and how p27 affects the conformation of mature RSV F. Monoclonal antibodies against p27, site Ø (pre-F specific), and site II were used to monitor RSV F conformation by enzyme-linked immunosorbent assay (ELISA) and imaging flow cytometry. Pre-F to post-F conformational change was induced by a temperature stress test. We found that p27 cleavage efficiency was lower on sucrose-purified RSV/A (spRSV/A) than on spRSV/B. In addition, cleavage of RSV F was cell line dependent: HEp-2 cells had higher retention of p27 than did A549 cells when infected with RSV. Higher levels of p27 were also found on RSV/A-infected cells than on RSV/B-infected cells. We observed that RSV/A F with higher p27 levels could better sustain the pre-F conformation during the temperature stress challenge in both spRSV- and RSV-infected cell lines. Our findings suggest that despite F sequence similarity, p27 of RSV subtypes was cleaved with different efficiencies, which were also dependent on the cell lines used for infection. Importantly, the presence of p27 was associated with greater stability of the pre-F conformation, supporting the possibility that RSV has more than one mechanism for fusion to the host cell. IMPORTANCE RSV fusion protein (F) plays an important role in entry and viral fusion to the host cell. The F undergoes proteolytic cleavages releasing a 27-amino-acid peptide (p27) to become fully functional. The role of p27 in viral entry and the function of the partially cleaved F containing p27 has been overlooked. p27 is thought to destabilize the F trimers, and thus, there is need for a fully cleaved F. In this study, we detected p27 on purified RSV virions and on the surface of virus-infected HEp-2 and A549 cells for circulating RSV strains of both subtypes. Higher levels of partially cleaved F containing p27 better sustained the pre-F conformation during the temperature stress challenge. Our findings highlight that the cleavage efficiency of p27 is different between RSV subtypes and among cell lines and that the presence of p27 contributes to the stability of the pre-F conformation.

Unswitched memory B cell deficiency in children with sickle cell disease and response to pneumococcal polysaccharide vaccine.

Early mortality in sickle cell disease (SCD) is attributed to increased infections due to loss of splenic function. Marginal zone B cells are important for initial opsonization of pathogens and can be absent in spleen histopathology in SCD. The frequency of unswitched memory B cells (UMBC), the circulating correlate of marginal zone B cells, reflects the immunologic function of the spleen. We hypothesized that asplenia in SCD is associated with alterations in the peripheral blood lymphocyte population and explored whether UMBC deficiency was associated with a clinical phenotype. We analyzed B cell subsets and clinical history for 238 children with SCD and 63 controls. The median proportion of UMBCs was lower in children with SCD compared with controls (4.7% vs. 6.6%, p < .001). Naïve B cells were higher in SCD compared with controls (80.6 vs. 76.3%, respectively, p = .02). UMBC frequency declined by 3.4% per year increase in age in SCD (95% CI: 2%, 4.7%, p < .001), but not in controls. A majority of children in all cohorts had an IgM concentration in the normal range for age and there were no differences between groups (p = .13). Subjects developed titers adequate for long-term protection to fewer serotypes in the polysaccharide vaccine than controls (14.7 vs. 19.4, p < .001). In this cohort, bacteremia was rare and specific clinical complications were not associated with UMBC proportion. In summary, UMBC deficiency occurs in SCD and is associated with age. Future studies should investigate B cell subsets prospectively and identify the mechanism of B cell loss in the spleen.

Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

[This corrects the article DOI: 10.1371/journal.pgen.1009679.].

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease.

Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.

Elastocaloric Effect in Graphene Kirigami.

Kirigami, a traditional Japanese art of paper cutting, has recently been explored for its elastocaloric effect (ECE) in kirigami-based materials (KMs), where an applied strain induces temperature changes. Importantly, the feasibility of a nanoscale graphene kirigami monolayer was experimentally demonstrated. Here, we investigate the ECE in GK representing the thinnest possible KM to better understand this phenomenon. Through molecular dynamics simulations, we analyze the temperature change and coefficient of performance (COP) of GK. Our findings reveal that while GKs lack the intricate temperature changes observed in macroscopic KMs, they exhibit a substantial temperature change of approximately 9.32 K (23 times higher than that of macroscopic KMs, which is about 0.4 K) for heating and -3.50 K for cooling. Furthermore, they demonstrate reasonable COP values of approximately 1.57 and 0.62, respectively. It is noteworthy that the one-atom-thick graphene configuration prevents the occurrence of the complex temperature distribution observed in macroscopic KMs.

Fish chorus variation in a tropical estuarine environmenta).

Fish choruses are still understudied in the Southwestern Atlantic Ocean. Temporal and spatial variation of fish choruses at two sites inside Guanabara Bay were investigated between 2021 and 2022; one sampling site was in a Marine Protected Area (MPA), and the other was in a rocky environment closer to vessel trafficking areas. Acoustic recordings were performed on 17 sampling occasions of 24 h, coupled to a temperature data logger. Long-term spectral averages were employed to determine choruses' start, end, and peak times, and third-octave levels were used to characterize spectral characteristics. Fish sounds were also analyzed and investigated with a principal components analysis. Choruses in the MPA lasted, on average, 4.5 h and had a peak frequency of 547.2 ± 226.6 kHz with a peak level of 104.6 ± 8.7 dB re 1 µPa. In contrast, the rocky site choruses lasted 5.5 h on average and had a peak frequency of 371.7 ± 131.0 Hz with a peak level of 113.4 ± 4.0 dB re 1 µPa. Chorus peak frequency was positively correlated to temperature (r = 0.4). Different types of fish sounds were identified, with some acoustics parameters varying between sites. Results indicate more than one chorusing species that may react to different factors.

Functional Magnetic Resonance Imaging Signal Variability Is Associated With Neuromodulation in Fibromyalgia.

OBJECTIVES: Although primary motor cortex (M1) transcranial direct current stimulation (tDCS) has an analgesic effect in fibromyalgia (FM), its neural mechanism remains elusive. We investigated whether M1-tDCS modulates a regional temporal variability of blood-oxygenation-level-dependent (BOLD) signals, an indicator of the brain's flexibility and efficiency and if this change is associated with pain improvement. MATERIALS AND METHODS: In a within-subjects cross-over design, 12 female FM patients underwent sham and active tDCS on five consecutive days, respectively. Each session was performed with an anode placed on the left M1 and a cathode on the contralateral supraorbital region. The subjects also participated in resting-state functional magnetic resonance imaging (fMRI) at baseline and after sham and active tDCS. We compared the BOLD signal variability (SDBOLD), defined as the standard deviation of the BOLD time-series, between the tDCS conditions. Baseline SDBOLD was compared to 15 healthy female controls. RESULTS: At baseline, FM patients showed reduced SDBOLD in the ventromedial prefrontal cortex (vmPFC), lateral PFC, and anterior insula and increased SDBOLD in the posterior insula compared to healthy controls. After active tDCS, compared to sham, we found an increased SDBOLD in the left rostral anterior cingulate cortex (rACC), lateral PFC, and thalamus. After sham tDCS, compared to baseline, we found a decreased SDBOLD in the dorsomedial PFC and posterior cingulate cortex/precuneus. Interestingly, after active tDCS compared to sham, pain reduction was correlated with an increased SDBOLD in the rACC/vmPFC but with a decreased SDBOLD in the posterior insula. CONCLUSION: Our findings suggest that M1-tDCS might revert temporal variability of fMRI signals in the rACC/vmPFC and posterior insula linked to FM pain. Changes in neural variability would be part of the mechanisms underlying repetitive M1-tDCS analgesia in FM.

New strategies for targeting kinase networks in cancer.

Targeted strategies against specific driver molecules of cancer have brought about many advances in cancer treatment since the early success of the first small-molecule inhibitor Gleevec. Today, there are a multitude of targeted therapies approved by the Food and Drug Administration for the treatment of cancer. However, the initial efficacy of virtually every targeted treatment is often reversed by tumor resistance to the inhibitor through acquisition of new mutations in the target molecule, or reprogramming of the epigenome, transcriptome, or kinome of the tumor cells. At the core of this clinical problem lies the assumption that targeted treatments will only be efficacious if the inhibitors are used at their maximum tolerated doses. Such aggressive regimens create strong selective pressure on the evolutionary progression of the tumor, resulting in resistant cells. High-dose single agent treatments activate alternative mechanisms that bypass the inhibitor, while high-dose combinatorial treatments suffer from increased toxicity resulting in treatment cessation. Although there is an arsenal of targeted agents being tested clinically and preclinically, identifying the most effective combination treatment plan remains a challenge. In this review, we discuss novel targeted strategies with an emphasis on the recent cross-disciplinary studies demonstrating that it is possible to achieve antitumor efficacy without increasing toxicity by adopting low-dose multitarget approaches to treatment of cancer and metastasis.

Scalable Synthesis and Characterization of Multilayer γ-Graphyne, New Carbon Crystals with a Small Direct Band Gap.

γ-Graphyne is the most symmetric sp2/sp1 allotrope of carbon, which can be viewed as graphene uniformly expanded through the insertion of two-carbon acetylenic units between all the aromatic rings. To date, synthesis of bulk γ-graphyne has remained a challenge. We here report the synthesis of multilayer γ-graphyne through crystallization-assisted irreversible cross-coupling polymerization. A comprehensive characterization of this new carbon phase is described, including synchrotron powder X-ray diffraction, electron diffraction, lateral force microscopy, Raman spectroscopy, infrared spectroscopy, and cyclic voltammetry. Experiments indicate that γ-graphyne is a 0.48 eV band gap semiconductor, with a hexagonal a-axis spacing of 6.88 Å and an interlayer spacing of 3.48 Å, which is consistent with theoretical predictions. The observed crystal structure has an aperiodic sheet stacking. The material is thermally stable up to 240 °C but undergoes transformation at higher temperatures. While conventional 2D polymerization and reticular chemistry rely on error correction through reversibility, we demonstrate that a periodic covalent lattice can be synthesized under purely kinetic control. The reported methodology is scalable and inspires extension to other allotropes of the graphyne family.

The cell biologist's guide to super-resolution microscopy.

Fluorescence microscopy has become a ubiquitous method to observe the location of specific molecular components within cells. However, the resolution of light microscopy is limited by the laws of diffraction to a few hundred nanometers, blurring most cellular details. Over the last two decades, several techniques - grouped under the 'super-resolution microscopy' moniker - have been designed to bypass this limitation, revealing the cellular organization down to the nanoscale. The number and variety of these techniques have steadily increased, to the point that it has become difficult for cell biologists and seasoned microscopists alike to identify the specific technique best suited to their needs. Available techniques include image processing strategies that generate super-resolved images, optical imaging schemes that overcome the diffraction limit and sample manipulations that expand the size of the biological sample. In this Cell Science at a Glance article and the accompanying poster, we provide key pointers to help users navigate through the various super-resolution methods by briefly summarizing the principles behind each technique, highlighting both critical strengths and weaknesses, as well as providing example images.

Long-term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species.

We investigated whether a set of phylogeographical tracked emergent events of Orthocoronavirinae were related to developed, urban and polluted environments worldwide. We explored coronavirus records in response to climate (rainfall parameters), population density, CO2 emission, Human Developmental Index (HDI) and deforestation. We contrasted environmental characteristics from regions with spillovers or encounters of wild Orthocoronavirinae against adjacent areas having best-preserved conditions. We used all complete sequenced CoVs genomes deposited in NCBI and GISAID databases until January 2021. Except for Deltacoronavirus, concentrated in Hong Kong and in birds, the other three genera were scattered all over the planet, beyond the original distribution of the subfamily, and found in humans, mammals, fishes and birds, wild or domestic. Spillovers and presence in wild animals were only reported in developed/densely populated places. We found significantly more occurrences reported in places with higher HDI, CO2 emission, or population density, along with more rainfall and more accentuated seasonality. Orthocoronavirinae occurred in areas with significantly higher human populations, CO2 emissions and deforestation rates than in adjacent locations. Intermediately disturbed ecosystems seemed more vulnerable for Orthocoronavirinae emergence than forested regions in frontiers of deforestation. Sadly, people experiencing poverty in an intensely consumerist society are the most vulnerable.

Surgical management of locally advanced breast cancer: Recommendations of the Brazilian Society of Surgical Oncology.

The Brazilian Society of Surgical Oncology organized a group of oncological surgeons to discuss surgical aspects associated with locally advanced breast carcinoma. This article reviews the indications, different surgeries (thoracoabdominal or myocutaneous flaps), and associated complications. It discusses special conditions such as invasion of the chest wall and interscapular thoracic disarticulation. It makes recommendations based on the literature regarding clinical findings, tumor conditions, response to neoadjuvant therapy, choice of flaps in surgery, and tumor biology.

Brazilian Society of Surgical Oncology surgical standards for resectable colorectal cancer liver metastases.

The management of colorectal cancer liver metastasis (CRLM) has become complex because of the increasing availability of medical, radiological, and surgical treatment options applied either alone or in combination. However, resection remains the only evidence-based curative therapy. These Brazilian Society of Surgical Oncology surgical standards are intended to guide clinicians in the decision-making process for modern surgical management of CRLM within a multidisciplinary team in an evidence-based framework, focusing on resectable disease.

Brazilian Society of Surgical Oncology guidelines for malignant bowel obstruction management.

BACKGROUND: Malignant bowel obstruction (MBO) is a frequent complication in advanced cancer patients and especially those with abdominal tumors. The clinical management of MBO requires a specific and individualized approach based on the disease prognosis. Surgery is recommended. Less invasive approaches such as endoscopic treatments should be considered when surgery is contraindicated. The priority of care for inoperable and consolidated MBO is to control the symptoms and promote the maximum level of comfort. OBJECTIVES: This study aimed to develop recommendations for the effective management of MBO. METHODS: A questionnaire was administered to all members of the Brazilian Society of Surgical Oncology, of whom 41 surgeons participated in the survey. A literature review of studies retrieved from the National Library of Medicine database was conducted on particular topics chosen by the participants. These topics addressed questions regarding the MBO management, to define the level of evidence and strength of each recommendation, and an adapted version of the Infectious Diseases Society of America Health Service rating system was used. RESULTS: Most aspects of the medical approach and management strategies reviewed were strongly recommended by the participants. CONCLUSIONS: Guidelines outlining the strategies for management MBO were developed based on the strongest evidence available in the literature.

Cancer risk-reducing surgery: Brazilian Society of Surgical Oncology Guideline Part 2 (Gastrointestinal and thyroid).

BACKGROUND: Risk-reducing operations are an important part of the management of hereditary predisposition to cancer. In selected cases, they can considerably reduce the morbidity and mortality associated with cancer in this population. OBJECTIVES: The Brazilian Society of Surgical Oncology (BSSO) developed this guideline to establish national benchmarks for cancer risk-reducing operations. METHODS: The guideline was prepared from May to December 2021 by a multidisciplinary team of experts to discuss the surgical management of cancer predisposition syndromes. Eleven questions were defined and assigned to expert groups that reviewed the literature and drafted preliminary recommendations. Following a review by the coordinators and a second review by all participants, the groups made final adjustments, classified the level of evidence, and voted on the recommendations. RESULTS: For all questions including risk-reducing colectomy, gastrectomy, and thyroidectomy, a major agreement was achieved by the participants, always using accessible alternatives. CONCLUSION: This and its accompanying article represent the first guideline in cancer risk reduction surgery developed by the BSSO and it should serve as an important reference for the management of families with cancer predisposition.

Chytrid fungus in amphibians from the lowland Brazilian Amazon.

Infectious diseases are one of the main threats to biodiversity. The fungus Batrachochytrium dendrobatidis (Bd) is associated with several amphibian losses around the globe, and environmental conditions may dictate the success of pathogen spread. The Brazilian Amazon has been considered climatically unsuitable for chytrid fungus, but additional information on Bd dynamics in this ecoregion is still lacking. We sampled 462 amphibians (449 anurans, 4 caudatans and 9 caecilians), representing 57 species from the Brazilian Amazon, and quantified Bd infections using qPCR. We tested whether abiotic variables predicted the risk of Bd infections, and tested for relationships between biotic variables and Bd. Finally, we experimentally tested the effects of Bd strains CLFT 156 and CLFT 102 (from the southern and northern Atlantic Forest, respectively) on Atelopus manauensis. We detected higher Bd prevalence than those previously reported for the Brazilian Amazon, and positive individuals in all 3 orders of amphibians sampled. Both biotic and abiotic predictors were related to prevalence, and no variable explained infection load. Moreover, we detected higher Bd prevalence in forested than open areas, while the host's reproductive biology was not a factor. We detected higher mortality in the experimental group infected with CLFT 156, probably because this strain was isolated from a region characterized by discrepant climatic conditions (latitudinally more distant) when compared with the host's sampling site in Amazon. The lowland Brazilian Amazon is still underexplored and future studies targeting all amphibian orders are essential to better understand Bd infection dynamics in this region.

Spatial structure of the Caatinga woody flora: abundance patterns have environmental, Pleistocene, and indigenous drivers.

Despite growing knowledge on the distribution and functioning of dryland vegetation types, their internal biodiversity structure (i.e., subregions) is much less studied. In the delineation of subregions, the use of species occurrence or abundance data may reveal different aspects of metacommunity structure. We revisit the issue of the bioregionalization of the woody flora of the Caatinga, the largest block of the dry forest and woodland biome in Latin America, using abundance data. We also evaluated the drivers of the spatial distribution of plant subregions: historical, current environmental and human effects. Using a K-means partition on interpolated NMDS axes, we identified 10 abundance subregions. Aridity, topography and soil, biome stability since the Pleistocene, and historical indigenous effects were retained by a Multinomial Logistic regression model, and their combined fractions explained most of the abundance variability in subregions. The subregions we present may support spatialized conservation and management decisions in the lack of detailed local data. The present results confirm the Caatinga woody flora broad composition patterns uncovered using presence-absence data in previous studies. Additionally, we found larger subregions than those identified with presence and absence data, suggesting the existence of oligarchies of dominant species in distinct parts of the Caatinga biome.

Sweetpotato Genotypes 'CIP BRS Nuti' and 'Canadense' Are Resistant to Meloidogyne incognita, M. javanica, and M. enterolobii.

Sweetpotato is a staple crop in Brazil presenting a smaller number of pathogens and diseases in comparison with other root and tuberous crops. Root-knot nematodes are among the most serious sweetpotato root pathogens. The impact of these pathogens also extends to succeeding crops. Because in Brazil, it is common to cultivate more than one crop per season, this problem is rapidly disseminated. The aim of this study was to assess the resistance of two sweetpotato clones and four commercial sweetpotato genotypes to three different Meloidogyne species. Assays were performed under greenhouse and field conditions. 'CIP BRS Nuti' and 'Canadense' were resistant to Meloidogyne incognita, M. javanica, and M. enterolobii under greenhouse conditions. This finding was obtained based on the reproduction factor < 0.2, meaning that the initial population of 5,000 nematodes was reduced to <1,000 individuals after 90 days of inoculation. Tomato and sweetpotato cultivar Beauregard, known to be susceptible to the three nematode species, were highly damaged by the pathogens. Similar results were also observed under field conditions. To our knowledge, 'CIP BRS Nuti' and 'Canadense' are the first South American commercial cultivars with triple nematode resistance.