Validation of Golden Gate Assemblies Using Highly Multiplexed Nanopore Amplicon Sequencing.

Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries of parts that can be combined into higher order assemblies allows engineering principles to be applied to biological systems. The basic parts, typically stored in Level 0 plasmids, are sequence validated by the method of choice and can be combined into higher order assemblies on demand. Higher order assemblies are typically transcriptional units, and multiple transcriptional units can be assembled into multi-gene constructs. Higher order Golden Gate assembly based on defined and validated parts usually does not introduce sequence changes. Therefore, simple validation of the assemblies, e.g., by colony polymerase chain reaction (PCR) or restriction digest pattern analysis is sufficient. However, in many experimental setups, researchers do not use defined parts, but rather part libraries, resulting in assemblies of high combinatorial complexity where sequencing again becomes mandatory. Here, we present a detailed protocol for the use of a highly multiplexed dual barcode amplicon sequencing using the Nanopore sequencing platform for in-house sequence validation. The workflow, called DuBA.flow, is a start-to-finish procedure that provides all necessary steps from a single colony to the final easy-to-interpret sequencing report.

Rapid growth rate of Enterobacter sp. SM3 determined using several methods.

BACKGROUND: Bacterial growth rate, commonly reported in terms of doubling time, is frequently determined by one of two techniques: either by measuring optical absorption of a growing culture or by taking samples at different times during their growth phase, diluting them, spreading them on agar plates, incubating them, and counting the colonies that form. Both techniques require measurements of multiple repeats, as well careful assessment of reproducibility and consistency. Existing literature using either technique gives a wide range of growth rate values for even the most extensively studied species of bacteria, such as Escherichia coli, Pseudomonas aeruginosa, and  Staphylococcus aureus. This work aims to apply several methods to reliably determine the growth rate of a recently identified species of Enterobacteriaceae, called Enterobacter sp. SM3, and to compare that rate with that of a well-known wildtype E. coli strain KP437. RESULTS: We extend conventional optical density (OD) measurements to determine the growth rate of Enterobacter sp. SM3. To assess the reliability of this technique, we compare growth rates obtained by fitting the OD data to exponential growth, applying a relative density method, and measuring shifts in OD curves following set factors of dilution. The main source of error in applying the OD technique is due to the reliance on an exponential growth phase with a short span. With proper choice of parameter range, however, we show that these three methods yield consistent results. We also measured the SM3 division rate by counting colony-forming units (CFU) versus time, yielding results consistent with the OD measurements. In lysogeny broth at 37oC, SM3 divides every 21 ± 3 min, notably faster than the RP437 strain of E. coli, which divides every 29 ± 2 min. CONCLUSION: The main conclusion of this report is that conventional optical density (OD) measurements and the colony-forming units (CFU) method can yield consistent values of bacterial growth rate. However, to ensure the reproducibility and reliability of the measured growth rate of each bacterial strain, different methods ought to be applied in close comparison. The effort of checking for consistency among multiple techniques, as we have done in this study, is necessary to avoid reporting variable values of doubling time for particular species or strains of bacteria, as seen in the literature.

Efficacy of nebulized GM-CSF inhalation in preventing oral mucositis in patients undergoing hematopoietic stem cell transplantation: A retrospective study.

Objective: To study the efficacy of oxygen atomization inhalation of granulocyte-macrophage colony-stimulating factor (GM-CSF) for preventing oral mucositis in patients following hematopoietic stem cell transplantation. Methods: Data from patients who received hematopoietic stem cell transplantation and were treated with GM-CSF for the prevention/treatment of oral mucositis in our hospital from June 2021 to June 2023 were collected. The enrolled patients were divided into an observation group and a control group according to the use of GM-CSF. The WHO Mucositis Scale Assessment Criteria were utilized to evaluate the characteristics of patients with oral mucositis (OM) from the beginning of the pretreatment period until they were discharged from the hospital. The general data, preconditioning protocol, transplantation method, overall grade and duration of oral mucositis, pain score, nutritional score and number of days of parenteral nutrition use, oral mucosal infection status and antibiotic use intensity, the granulocyte and megakaryocyte reconstruction time, and adverse reaction reports of the patients were collected and summarized through the medical records system. Results: A total of 143 patients were included in this study, including 75 patients in the observation group. In the observation group, there were 36 males and 39 females aged 22-67 years. There were 45 patients who received autologous transplantation and 30 patients who received allogeneic transplantation. In terms of the disease distribution, there were 33 cases of leukemia, 24 cases of lymphoma, 11 cases of multiple myeloma, and 8 other cases (3 cases of aplastic anemia, 2 cases of myelodysplastic syndrome, 2 cases of myelofibrosis, 1 case of POEMS syndrome). There were 68 patients in the control group, including 33 males and 35 females; the control group patients were aged 25-74years. Forty-one patients received autologous transplantation, and 27 patients received allogeneic transplantation. The disease distribution included 29 cases of leukemia, 17 cases of lymphoma, 12 cases of multiple myeloma, and 7 other cases (3 cases of aplastic anemia, 2 cases of myelodysplastic syndrome, 1 case of myelofibrosis, 1 case of POEMS syndrome). There were no significant differences between the two groups concerning age, sex, disease distribution or the transplantation method (P > 0.05). In the observation group, 13 cases did not develop oral mucositis, and 32 cases developed oral mucositis (16 cases of Grade I, 14 cases of Grade II, 2 cases of Grade III, and 0 cases of Grade IV). In the control group, there were 5 cases without mucositis and 36 cases with oral mucositis (6 cases of Grade Ⅰ, 16 cases of Grade Ⅱ, 8 cases of Grade Ⅲ, and 6 cases of Grade Ⅳ), the difference was statistically significant (P < 0.05). The pain score and duration of mucositis in the observation group were significantly lower than those in the control group (P < 0.05). In addition, the oral infection rate, antibiotic use intensity, nutritional score, per capita number of days of parenteral nutrition use and hematopoietic reconstruction time in the observation group were significantly lower than those in the control group (P < 0.05). In the observation group, 8 patients did not develop oral mucositis, and 22 patients developed oral mucositis (13 cases of Grade I, 7 cases of Grade II, 1 case of Grade III, and 1 case of Grade IV). In the control group, 1 case did not develop mucositis, and 26 cases developed oral mucositis (3 cases of Grade Ⅰ, 10 cases of Grade Ⅱ, 9 cases of Grade Ⅲ, and 4 cases of Grade Ⅳ). The difference was statistically significant (P < 0.05). The pain score and duration of mucositis in the observation group were significantly lower than those in the control group (P < 0.05). In addition, the oral mucosal infection rate, antibiotic use intensity, nutritional score, per capita number of days of parenteral nutrition use and hematopoietic reconstruction time in the observation group were significantly lower than those in the control group (P < 0.05). No adverse reactions were reported in either group. Conclusion: In both autologous transplantation and allogeneic transplantation patients, GM-CSF atomized inhalation can improve the prevention and treatment of oral mucositis in stem cell transplantation patients, reduce the incidence of oral infection, reduce the intensity of antibiotic use and the number of days of parenteral nutrition use, and thus promote the process of hematopoietic reconstruction.

Frequently Touched Sites in the Intensive Care Unit Environment Returning 100 Colony-Forming Units per Surface Area Sampled Are Associated With Increased Risk of Major Bacterial Pathogen Detection.

BACKGROUND: A threshold for surface hygiene has not been defined for the healthcare arena. We aimed to identify the magnitude of bacterial contamination of frequently touched sites in the intensive care unit (ICU) environment that could be used to guide quality improvement initiatives. METHODS: Nineteen patients in a mixed ICU environment (providing care for medical and surgical patients) were followed from admission for 72 hours in 2010. Baseline cultures of frequently touched environmental sites were obtained at time zero following active decontamination and at 12, 24, 48, and 72 hours without further disinfection. We tested for an association of environmental reservoirs returning ≥ 100 colony-forming units (CFU) per surface area sampled with major bacterial pathogen detection. RESULTS: There were 446 ICU room, day, and reservoir combinations sampled from 19 patients. There were pathogens detected in 40% (79/199) of samples with ≥ 100 CFU vs. 14% (35/247) of samples returning < 100 CFU. The relative risk was 2.80 (95% CI: 1.97-3.98, P <0.0001). The odds ratio adjusted for time in hours was 3.11 (95% CI: 1.84-5.34, P < 0.0001). CONCLUSIONS: Frequently touched ICU environmental sites returning ≥ 100 CFU are associated with major bacterial pathogen detection. This threshold for surface hygiene can be used to ensure compliance with ICU environmental cleaning protocols and to guide quality improvement initiatives.

An artificial bee colony optimization algorithms for solving fuzzy capacitated logistic distribution center problem.

This paper presents a methodological approach to solving the fuzzy capacitated logistic distribution center problem, with a focus on the optimal selection of distribution centers to meet the demands of multiple plants. The distribution centers are characterized by fixed costs and capacities, while plant demands are modeled using fuzzy triangular membership functions. The problem is mathematically formulated by converting fuzzy demands into crisp values, providing a structured framework for addressing uncertainty in logistic planning. To support future research and facilitate comparative analysis, 20 benchmark problems were generated, filling a gap in the existing literature. Three distinct artificial bee colony algorithm variants were hybridized with a heuristic: one using the best solution per iteration, another incorporating chaotic mapping and adaptive procedures, and the third employing convergence and diversity archives. An experimental design based on Taguchi's orthogonal arrays was employed for optimizing the algorithm parameters, ensuring systematic exploration of the solution space. The developed methods offer a comprehensive toolkit for addressing complex, uncertain demands in logistic distribution, with code provided for reproducibility. Key contributions include:•Development of a fuzzy model for the selection of distribution centers with fixed costs and capacities under uncertain plant demands.•Generation of 20 benchmark problems to advance research in the fuzzy capacitated logistic distribution center problem domain.•Integration of a heuristic approach with three distinct ABC algorithm variants, each contributing unique methodological insights.

Changes in roosting decisions and group structure following parturition in little brown myotis (Myotis lucifugus).

In many temperate animals, reproductive cycles coincide with seasonal weather changes resulting in behaviour changes such as movement and habitat selection. In social species, these physiological and environmental changes can alter the costs and benefits of social interactions, impacting the structure of animal groups. In little brown myotis (Myotis lucifugus), a gregarious bat occupying much of North America, the pregnancy and lactation phases present different challenges to energy balance and maternal movement, and reduced forage distance has been observed during the lactation period. As such, we hypothesized that differences between reproductive phases alter the roost switching decisions of individual bats and therefore the overall group structure of little brown myotis maternity colonies. We observed that adult females were less likely to switch roosts during the lactation period even when accounting for changing weather conditions. This shift in roost switching behaviour may be the source of observed differences in group structure between reproductive periods. We reported a decline in network cohesiveness, but no meaningful variation in individual roost fidelity and association strengths of dyads between reproductive phases. These results support the contention that reproductive processes in female little brown myotis influence sociality and overall roosting patterns within maternity groups.

Inhibition of CEACAM1 expression in cytokine-activated neutrophils using JAK inhibitors.

OBJECTIVES: Carcinoembryonic-antigen-related cell-adhesion molecule 1 (CEACAM1) is an adhesion molecule that acts as a coinhibitory receptor in the immune system. We previously demonstrated that CEACAM1 is predominantly expressed on peripheral blood neutrophils in patients with RA. The aim of the present study was to investigate the effects of Janus kinase inhibitors (JAKi) on cytokine-activated human neutrophils and CEACAM1 expression. METHODS: Peripheral blood neutrophils were obtained from healthy subjects. Isolated neutrophils were stimulated with tumor necrosis factor-alpha (TNF-α) or granulocyte-macrophage colony-stimulating factor (GM-CSF) in the presence or absence of JAKi. The expression of CEACAM1 in peripheral blood neutrophils was analyzed by flow cytometry. Protein phosphorylation of signal transducer and activator of transcription (STAT)1, STAT3, and STAT5 was assessed by western blot using phospho-specific antibodies. RESULTS: We found that TNF-α-induced CEACAM1 expression was marginally suppressed after pretreatment with pan-JAK inhibitor, tofacitinib. Moreover, TNF-α induced STAT1 and STAT3 phosphorylation at the late stimulation phase (4 to 16 h). The expressions of CEACAM1 on neutrophils were markedly up-regulated by GM-CSF not by interleukin (IL)-6 stimulation. All JAKi inhibited GM-CSF-induced CEACAM1 expressions on neutrophils, however, the inhibitory effects of baricitinib were larger compared to those of tofacitinib or filgotinib. Moreover, CEACAM1 was marginally upregulated in interferon (IFN)-γ stimulated neutrophils. Similarly, JAKi inhibited IFN-γ-induced CEACAM1 expressions on neutrophils. CONCLUSIONS: We demonstrated that JAKi prevent GM-CSF-induced CEACAM1 expression in neutrophils, and JAKi-induced inhibition depends on their selectivity against JAK isoforms. These findings suggest that JAKi can modulate the expression of CEACAM1 in cytokine-activated neutrophils, thereby limiting their activation.

Identification and management of infections caused by Giardia sp., Trichuris sp. and Demodex sp. in captive Brazilian porcupines (Coendou prehensilis).

The Brazilian porcupine (Coendou prehensilis, Rodentia, Erethizontidae) is an arboreal South American nocturnal rodent. Switzerland is home to one of the largest captive colonies in Europe. In June 2022, most of the animals in this colony showed severe diarrhoea, and Giardia sp. cysts were detected. All the animals were treated with metronidazole (75 mg/animal/day orally) for five days, repeating after two weeks. The diarrhoea continued, sometimes containing blood, and further analyses revealed Giardia sp. cysts and Trichuris sp. eggs with a particular undulating eggshell in pooled samples. The soil layer of some enclosures was removed to thoroughly clean and disinfect the underlying concrete floor. The animals were treated with fenbendazole (50 mg/kg/day orally) for 5 days repeating after three days. Giardia sp. cysts were not further detected. However, Trichuris sp. eggs were detected in branch bark samples and in six animals 2-3 months after treatment. The treatment with fenbendazole was repeated and no further Trichuris sp. eggs were detected. A 18S rRNA fragment consensus sequence showed 98.58% identity with Trichuris fossor. The Trichuris sp. in C. prehensilis may represent a new species, specific for arboreal porcupines. Demodex mites were observed in faecal flotations and thereafter in skin scrapings from five animals (four of them being family-related). A 16S consensus sequence showed 86.4% identity with other Demodex species. The animals were initially treated with moxidectin (0.4 and 0.8 mg/kg orally) and afterwards with sarolaner (10 mg/animal) but the treatments were not completely effective since in control scrapings, two animals evidenced few non-motile mites. An individual susceptibility and poor immunological control of the infection is suggested. Treatment with fenbendazole was effective against Giardia sp. and Trichuris sp. infections; however, reinfections may occur if the enclosures and tree branches are not deep cleaned and disinfected or replaced.

Survival strategies of microalgae in response to fluctuating brine environments in Saroma-ko Lagoon sea ice, Hokkaido, Japan.

This study investigated the changes in sea ice temperature, microalgae species distribution, shape changes, and photosynthetic activity observed in the first-year ice that forms in winter in Saroma-ko Lagoon, Hokkaido, Japan. Temperatures at the bottom of the ice remained constant at -1.7°C, near the freezing point, while they varied between -6 and -1°C with diel fluctuations at the surface layer. Carefully collected algal samples showed high photosynthetic quantum yield and acclimation to the light intensities of individual ice layers; this indicates that the algal photosynthetic activity responds to dynamic changes in the ice environment, such as variations in temperature, salinity, and brine space. The algal communities consisted of more than 95% diatoms. Smaller algal cells were distributed in the upper layer of the sea ice compared to the lower layers. Chaetoceros sp., the dominant small-cell species, was evenly distributed throughout the layers. In contrast, Detonula confervacea, the dominant large-cell species, was unevenly distributed in the lower layer, with smaller colony size and cell volume in the upper layer. The shape differences observed in this species were thought to be a response to the changing environment within the first-year sea ice.

ECG arrhythmia classification based on the fast ant colony clustering algorithm with improved spatiotemporal feature perception ability.

Electrocardiograph (ECG) is one of the most critical physiological signals used for arrhythmia diagnosis. In recent years, ECG arrhythmia classification devices consisting of multi-module sensors, clustering algorithms and neural networks play an important role in monitoring and diagnosing cardiovascular diseases. However, the commonly used ECG arrhythmia classification methods are still facing some problems such as the complex model structure and long running time. To address the above problems, this paper proposes an ECG arrhythmia classification method based on the fast ant colony clustering algorithm with improved spatiotemporal feature perception ability (SFP-FACC), which uses LSTM to fit the cluster centers and avoids the time consumption of updating the cluster centers during the classification process. The spatiotemporal feature perception ability of this model with the dynamic time warping (DTW) algorithm is improved. The classification is achieved by applying the combination of Euclidean distance and DTW. The convergence speed of the model is improved by using dynamic pheromone volatility coefficient; and finally the optimal solution of the model is determined by using radix sort. Based on the MIT-BIH arrhythmia dataset, the overall accuracy of the proposed classification method in this paper achieves 99.04 %, and even the accuracy of certain types of classification achieves 100 %, and the running time is about 3.5 times faster than that of the basic models. The experiments show that the method proposed in this paper has certain advantages.

The transplantation effect of pegylated granulocyte colony-stimulating factor mobilized hematopoietic stem cells may be superior to that of G-CSF mobilized hematopoietic stem cells in haploidentical allogeneic hematopoietic cell transplantation.

Granulocyte colony-stimulating factor (G-CSF) mobilized peripheral blood stem cells have become the preferred source of hematopoietic stem cells. We compared the effectiveness of G-CSF and pegylated G-CSF (peg-G-CSF) for hematopoietic stem cell mobilization in haploidentical hematopoietic stem cell transplantation (haplo-HSCT) donors, and evaluated the transplant outcomes. We conducted a matched retrospective cohort study. Donors mobilized with peg-G-CSF (n = 70) and G-CSF (n = 70). 140 consecutive patients diagnosed with acute leukemia who underwent haplo-HSCT were included in this study. The findings revealed that the peg-G-CSF cohort exhibited significantly elevated myeloid-derived suppressor cells (MDSCs) levels in their grafts when compared to the G-CSF cohort (P < 0.001). The 100-day cumulative incidence (CI) of grade III-IV acute graft-versus-host disease (GVHD) and 1-year CI of moderate-to-severe chronic GVHD were 4.3% vs 14.3 % (P = 0.047) and 11.2% vs 27.4 % (P = 0.023), in the peg-G-CSF group and G-CSF group. Patients reveiving mobilized stem cell with peg-G-CSF had a significantly greater likelihood of 1-year GVHD-free relapse-free survival (GRFS) compared to patients reveiving mobilized stem cell with G-CSF (74.9% vs 37.9 %, P < 0.001). The higher graft MDSCs proportion was associated with lower grade II-IV aGVHD, cGVHD (P < 0.05) and higher GRFS in the univariate analysis (P < 0.05). Multivariate analysis showed that MDSCs proportion higher than 11.36 % (HR, 0.305; 95 % CI, 0.154-0.606; P = 0.001) and peg-G-CSF for stem cell mobilization (HR, 0.466; 95 % CI, 0.251-0.865; P = 0.016) were independent prognostic factors of GRFS. The superior survival rates observed in recipients of peg-G-CSF-mobilized cells are likely due to reduced acute GVHD, potentially mediated by the increased MDSCs within the grafts.

Adaptation of feeding behaviors on two Brassica species by colonizing and noncolonizing Bemisia tabaci (Hemiptera: Aleyrodidae) NW whiteflies.

Bemisia tabaci New World (NW) (Gennadius) (Hemiptera: Aleyrodidae), a whitefly in the B. tabaci species complex, is polyphagous on many plant species. Yet, it has been displaced, albeit not entirely, by other whitefly species. Potential causes could include issues with adaptation, feeding, and the colonization of new-hosts; however, insights that would help clarify these possibilities are lacking. Here, we sought to address these gaps by performing electropenetrography (EPG) recordings of NW whiteflies, designated "Napus" and "Rapa," reared on 2 colony hosts, Brassica napus and B. rapa, respectively. Analysis of 17 probing and pathway (pw) phase-related EPG variables revealed that the whiteflies exhibited unique probing behaviors on their respective colony hosts, with some deterrence being encountered on B. rapa. Upon switching to B. rapa and B. napus, the probing patterns of Napus and Rapa whiteflies, respectively, adapted quickly to these new-hosts to resemble that of whiteflies feeding on their colony hosts. Results for 3 of the EPG variables suggested that B. rapa's deterrence against Napus whitefly was significant prior to the phloem phase. This also suggested that adaptation by Rapa whitefly improved its pw probing on B. rapa. Based on analysis of 24 phloem phase-related EPG variables, Napus and Rapa whiteflies performed equally well once they entered phloem phase and exhibited comparable phloem acceptability on both the colony- and new-hosts. These findings demonstrate that NW whiteflies reared on a colony host are highly adaptable to feeding on a new host despite encountering some deterrence during the nonphloem phases in B. rapa plant.

Optimized protocol for collecting root canal biofilms for in vitro studies.

Endodontic retreatment is often necessitated by several factors, including the persistence of microorganisms in the root canal system (RCS). Their complex organization in biofilms increases their pathogenic potential, necessitating new disinfection strategies. This study aimed to standardize a new in vitro protocol for collecting biofilm from the RCS. Thirty-four bovine incisors were used in the study, divided into two experimental groups with two collection steps each: (a) biofilm collection protocol and (b) absorbent paper points protocol. Twelve specimens from each group were selected for counting colony-forming units (CFUs), while eight specimens were prepared for scanning electron microscopy (SEM). Two additional specimens served as sterilization controls to ensure that experiments were free of contamination. The coronal region was removed and standardized at 15 mm. After preparation with ProTaper up to F5, the apical foramen was sealed with composite resin, and the roots were stabilized with acrylic resin in 1.5-mL Eppendorf tubes. The specimens were sterilized and inoculated with Enterococcus faecalis NTCT 775 every 24 h for 21 days. After this period, each group underwent biofilm collection protocols, and CFU and scanning electron microscopy (SEM) data were analyzed. The Shapiro-Wilk test was performed to assess the normality of log-transformed data, and the results indicated a normal distribution for all groups, allowing parametric testing. The Levene test was used to evaluate the equality of variances. The proposed biofilm collection method yielded significantly higher CFU counts compared with the absorbent paper points method, particularly when analyzed on a log10 scale. An independent samples t-test confirmed a statistically significant difference between the two methods (p < 0.0001). The proposed protocol achieved an efficiency rate of 95.85 % ± 1.15 %, whereas the absorbent paper points protocol yielded a lower efficiency of 5.46 % ± 1.37 %. Therefore, the biofilm collection protocol proposed in this study proved to be more effective for biofilm removal from the RCS.

Deubiquitinating enzyme USP39 promotes the growth and metastasis of gastric cancer cells by modulating the degradation of RNA-binding protein RBM39.

It has been revealed recently that the RNA-binding motif protein RBM39 is highly expressed in several cancers, which results in poor patient survival. However, how RBM39 is regulated in gastric cancer cells is unknown. Here, affinity purification-mass spectrometry and a biochemical screening are employed to identify the RBM39-interacting proteins and the deubiquitinating enzymes that regulate the RBM39 protein level. Integration of the data obtained from these two approaches uncovers USP39 as the potential deubiquitinating enzyme that regulates RBM39 stability. Bioinformatic analysis discloses that USP39 is increased in gastric cancer tissues and its elevation shortens the duration of overall survival for gastric cancer patients. Biochemical experiments verify that USP39 and RBM39 interact with each other and highly colocalize in the nucleus. Expression of USP39 elevates while USP39 knockdown attenuates the RBM39 protein level and their interaction regulates this modulation and their colocalization. Mechanistic studies reveal that USP39 reduces the K48-linked polyubiquitin chains on RBM39, thus enhancing its stability and increasing the protein level by preventing its proteasomal degradation. USP39 overexpression promotes while its knockdown attenuates the growth, colony formation, migration, and invasion of gastric cancer cells. Interestingly, overexpression of RBM39 partially restores the impact of USP39 depletion, while RBM39 knockdown partially abolishes the effect of USP39 overexpression on the growth, colony formation, migration, and invasion of gastric cancer cells. Collectively, this work identifies the first DUB for RBM39 and elucidates the regulatory functions and the underlying mechanism, providing a possible alternative approach to suppressing RBM39 by inhibiting USP39 in cancer therapy.

Optimized medium conditions maximize colony regeneration from a single cell of Botryococcus braunii NIES836.

Botryococcus braunii is a colonial alga recognized for its slow growth but high hydrocarbon accumulation. Although using genetic engineering to increase the growth rate and hydrocarbon yield of B. braunii is desirable, the presence of an extracellular matrix (ECM) significantly hinders the emergence of a homogeneous colony from a single DNA-transformed cell. Previously, we developed a method to isolate single cells without ECM from colonies. However, following the isolation of single cells, several months are required to regenerate colonies with a sufficient cell mass for subsequent analysis. To shorten the colony regeneration period, we investigated basal media and medium components, along with growth-promoting additives, in a series of single-factor experiments and optimized the concentrations of the medium constituents via response surface methodology (RSM). The results of the single-factor experiments revealed that the nitrogen source (a mixture of NaNO3 and NH4NO3), 1-naphthylacetic acid (NAA) and Fe(III)-citrate significantly increased the growth of B. braunii single cells into colonies. The optimal medium composition identified by RSM included 151.6 mg/L nitrogen source, 2.419 mg/L NAA and 15.3 mg/L Fe(III)-citrate. Verification experiments showed that the optimized medium resulted in a 1.75-fold increase in colony size compared with that of colonies grown in nonoptimized AF6 medium. This is the first report of the optimal medium composition for the regeneration of B. braunii colonies from single cells.

Causal network linking honey bee (Apis mellifera) winter mortality to temperature variations and Varroa mite density.

Winter season is a critical time for honey bees (Apis mellifera) colonies when individual mortalities may lead to total colony losses or diminish productivity in subsequent seasons. A deeper understanding of the causes and consequences of winter mortality is required. In this study, we analyzed winter (November-March) individual bee mortality in an apiary in Central Europe from 1991 to 2023. We observed consistency in mortality times among years, but also some systematic departures from the shared trend. We distinguished four clusters of year-specific mortality trajectories. However, we found no statistically significant differences in means of spring (March-May), autumn (October), winter (November-March) temperatures, or autumn Varroa destructor density among clusters. Nevertheless, our insights into the dynamics of individual bee mortality may be important for determining critical moments during wintering when implementing additional protective measures could prove beneficial. Hypothesis-driven path analysis indicated causal links in our study system, including both direct and indirect influences. The density of V. destructor in autumn was positively related to temperature, especially in the preceding spring, but to a lesser extent also in autumn. Increased winter mortality was related to lower winter temperatures and a higher mite infestation in autumn. We found no significant effects of individual winter mortality on honey harvests in subsequent seasons. Honey harvest was determined by bee abundance in spring, and the latter, unexpectedly, was not related to winter mortality. Our study adds to accumulating evidence of the major role of weather and climatic conditions in the resilience of honey bee colonies and improves our understanding of mortality processes. We highlighted the importance of causative factors, especially seasonal temperatures and V. destructor density, and their potential as predictive indicators of individual winter mortality, bee colony fate, and honey productivity.

Do diet and Fumagillin treatment impact Vairimorpha (Nosema) spp. (Microspora: Nosematidae) infections in honey bees (Hymenoptera: Apidae) and improve survival and growth of colonies overwintered in cold storage?

Vairimorpha (Microsporidia: Nosematidae) is a microsporidian that infects honey bees especially in winter. Fumagillin can reduce infections, but whether overwintering survival is improved is unclear. The diet also may influence the severity of Nosema infections. We examined the relationship between Nosema and colony size and survival in hives overwintered in cold storage facilities. In year 1, no Fumagillin treatments were applied. Colony size and survival after cold storage and almond bloom were comparable between groups with high and low pre-cold storage infections. In year 2, size and survival were compared among colonies with and without Fumagillin treatment that were fed either pollen or protein supplement prior to overwintering. Colonies treated with Fumagillin had lower spore numbers than untreated, but colony sizes and survival were similar among the treatments. However, more colonies with zero spores per bee could be rented for almond pollination and were alive after bloom than those averaging >1 million spores per bee. Fat body metrics can affect overwintering success. In both years, fat body weights and protein concentrations increased, and lipid concentrations decreased while bees were in cold storage. Fat body metrics did not differ with Nosema infection levels. However, Fumagillin negatively affected pre-cold storage fat body protein concentrations and colony sizes after cold storage and almond bloom. Treating with Fumagillin before overwintering in cold storage might result in greater colony survival if spore numbers are high, but undetectable or even negative effects when spore numbers are low.

Ant colony optimization: A bibliometric review.

This paper is a follow-up of one of the most-cited articles published in the first 20 years of the existence of Physics of Life Reviews. The specific topic is "ant colony optimization", which is a metaheuristic for solving challenging optimization problems. Due to its inspiration from natural ant colonies' shortest path-finding behavior, this optimization technique forms part of a larger field known as swarm intelligence. After a short introduction to ant colony optimization, we first provide a chronology focusing on algorithmic developments rather than applications. The main part of the paper deals with a bibliometric study of the ant colony optimization literature. Interesting trends concerning, for example, the geographic origin of publications and the change in research focus over time, can be learned from the presented graphs and numbers.

Causes of Musculoskeletal Pain in Paget's Disease of Bone.

Paget's disease of bone (PDB) is characterised by increased and disorganised bone remodelling leading to various complications, such as bone deformity, deafness, secondary osteoarthritis, and pathological fracture. Pain is the most common presenting symptom of PDB, but it is unclear to what extent this is due to increased metabolic activity of the disease, complications, or unrelated causes. We conducted a cross-sectional study of 168 people with PDB attending secondary care referral centres in the UK. We documented the presence of musculoskeletal pain and sought to determine its underlying causes. Musculoskeletal pain was reported by 122/168 (72.6%) individuals. The most common cause was osteoarthritis of joints distant from an affected PDB site in 54 (44.3%), followed by metabolically active PDB in 18 (14.7%); bone deformity in 14 (11.4%); osteoarthritis of a joint neighbouring an affected site in 11 (9.0%), neuropathic pain in 10 (8.2%), and various other causes in the remainder. Pain was more common in women (p<0.019) and in older individuals (p<0.001). Circulating concentrations of macrophage colony-stimulating factor (M-CSF) were significantly higher in those with pain (p = 0.008), but there was no difference between groups of patients with and without pain in concentrations of interleukin-6 (IL-6) or biochemical markers of bone turnover. Pain is a common symptom in PDB but is most often due to osteoarthritis at an unaffected site. The study illustrates the importance of fully evaluating people with PDB to determine the underlying cause of pain so that management can be tailored appropriately.

Pulmonary alveolar proteinosis complicated by lung cancer with favorable prognosis: a case report and literature review.

With the increasing incidence of lung cancer, the coexistence of pulmonary alveolar proteinosis (PAP) and lung cancer is becoming more common. However, the standard treatment protocols for patients with both conditions are still being explored. The conflict between the rapidly evolving therapeutic approaches for tumors and the limited treatment options for PAP presents a significant challenge for clinicians. Determining the optimal timing of treatment for both conditions to maximize patient benefit is a clinical conundrum. Here, we report a rare case of PAP complicated by lung adenocarcinoma, where interstitial lung changes worsened after neoadjuvant therapy but improved significantly following surgical resection of the lung adenocarcinoma. This case highlights the importance of prioritizing tumor treatment in patients with lung cancer complicated by PAP and examines the interplay between the two conditions, as well as potential therapeutic strategies.